I have my "Spawn Cap" settings below average: 90 total. How did my map spawn over 450 in an area? I must prevent this from happening. How do I enforce Spawn Caps to be true to their value? Is there a despawn enforcement to prevent this? Are Spawn Caps bugged?

15 Ambient
10 Creature
30 Monster
10 Opensky
10 Underground
15 Watercreature

90 Total

There's a few things you can do to help locate the problem

Check that JAS has spawned the all of those entities (many mods have their own spawners that need to be turned off in their respective configs. Lycanites and Mo'Creatures are just 2 examples).
-JAS commands are one useful tool (unless you used /jas killall or /jas countcap to get your figure of 450)
-turn on logging in LoggingProperties.cfg

If that IDs JAS as the culprit, please paste links to logs and configs.

If JAS isn't spawning the extras, it could be many things. If you've already checked other mods' spawners, then check to see if there's a particular type of entity or CreatureType that's spawning more than others. Does it spawn like that without JAS?

Lastly, check GlobalProperties.cfg. Are the VANILLA COMPATABILITY settings default?
(ie "Turn gamerule spawning off on start": false,
"Empty vanilla spawnlists": true,
"Disable Vanilla Chunk Spawning": true,)

Will /jas killall remove all or my Custom NPCs?

I eliminated the additional spawning from Mo'Creatures. Vanilla spawning doesn't seem to be doing anything on it's own so I have the CustomSpawn from JAS enabled and vanilla disabled. However I have run into an old issue that caused me to remove JAS before. I am hoping it is a config issue that will resolve things.

I have fish spawning on the ground and inside the ground. Note that I do have Aquatic Abyss mod and that doesn't seem to blend with JAS fully. I finally got the sea serpents to spawn but the don't do so in water. I also have a critical error that crashes my server at times until I remove an entity with NBTexploter. These entities have always been fish spawning with errors. See Crash log below.

---- Minecraft Crash Report ----
// Uh... Did I do that?

Time: 11/24/15 4:10 PM
Description: Ticking entity

java.lang.NullPointerException: Ticking entity
at thehippomaster.aquaticabyss.WaterCreature.func_70645_a(WaterCreature.java:218)
at net.minecraft.entity.EntityLivingBase.func_70097_a(EntityLivingBase.java:855)
at thehippomaster.aquaticabyss.Fish.func_70097_a(Fish.java:71)
at net.minecraft.entity.EntityLivingBase.func_70030_z(EntityLivingBase.java:198)
at net.minecraft.entity.EntityLiving.func_70030_z(EntityLiving.java:157)
at net.minecraft.entity.Entity.func_70071_h_(Entity.java:318)
at net.minecraft.entity.EntityLivingBase.func_70071_h_(EntityLivingBase.java:1561)
at net.minecraft.entity.EntityLiving.func_70071_h_(EntityLiving.java:206)
at thehippomaster.aquaticabyss.AquaticCreature.func_70071_h_(AquaticCreature.java:112)
at thehippomaster.aquaticabyss.WaterCreature.func_70071_h_(WaterCreature.java:64)
at net.minecraft.world.World.func_72866_a(World.java:2070)
at net.minecraft.world.WorldServer.func_72866_a(WorldServer.java:648)
at net.minecraft.world.World.func_72870_g(World.java:2034)
at net.minecraft.world.World.func_72939_s(World.java:1887)
at net.minecraft.world.WorldServer.func_72939_s(WorldServer.java:489)
at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:636)
at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:334)
at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:547)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:427)
at net.minecraft.server.MinecraftServer$2.run(MinecraftServer.java:685)

A detailed walkthrough of the error, its code path and all known details is as follows:

-- Head --
Stacktrace:
at thehippomaster.aquaticabyss.WaterCreature.func_70645_a(WaterCreature.java:218)
at net.minecraft.entity.EntityLivingBase.func_70097_a(EntityLivingBase.java:855)
at thehippomaster.aquaticabyss.Fish.func_70097_a(Fish.java:71)
at net.minecraft.entity.EntityLivingBase.func_70030_z(EntityLivingBase.java:198)
at net.minecraft.entity.EntityLiving.func_70030_z(EntityLiving.java:157)
at net.minecraft.entity.Entity.func_70071_h_(Entity.java:318)
at net.minecraft.entity.EntityLivingBase.func_70071_h_(EntityLivingBase.java:1561)
at net.minecraft.entity.EntityLiving.func_70071_h_(EntityLiving.java:206)
at thehippomaster.aquaticabyss.AquaticCreature.func_70071_h_(AquaticCreature.java:112)
at thehippomaster.aquaticabyss.WaterCreature.func_70071_h_(WaterCreature.java:64)
at net.minecraft.world.World.func_72866_a(World.java:2070)
at net.minecraft.world.WorldServer.func_72866_a(WorldServer.java:648)
at net.minecraft.world.World.func_72870_g(World.java:2034)

-- Entity being ticked --
Details:
Entity Type: aquaticabyss.fish (thehippomaster.aquaticabyss.CommonFish)
Entity ID: 4145
Entity Name: Fish
Entity's Exact location: -1292.50, 85.00, -14355.50
Entity's Block location: World: (-1293,85,-14356), Chunk: (at 3,5,12 in -81,-898; contains blocks -1296,0,-14368 to -1281,255,-14353), Region: (-3,-29; contains chunks -96,-928 to -65,-897, blocks -1536,0,-14848 to -1025,255,-14337)
Entity's Momentum: 0.00, -0.08, 0.00
Stacktrace:
at net.minecraft.world.World.func_72939_s(World.java:1887)
at net.minecraft.world.WorldServer.func_72939_s(WorldServer.java:489)

-- Affected level --
Details:
Level name: Wyldlans2
All players: 1 total; [EntityPlayerMP['Kharon_47'/3945, l='Wyldlans2', x=-1245.54, y=136.00, z=-14309.56]]
Chunk stats: ServerChunkCache: 1066 Drop: 0
Level seed: -8154567819696524531
Level generator: ID 04 - ATG, ver 0. Features enabled: true
Level generator options:
Level spawn location: World: (-34,64,-91), Chunk: (at 14,4,5 in -3,-6; contains blocks -48,0,-96 to -33,255,-81), Region: (-1,-1; contains chunks -32,-32 to -1,-1, blocks -512,0,-512 to -1,255,-1)
Level time: 98504074 game time, 10528399 day time
Level dimension: 0
Level storage version: 0x04ABD - Anvil
Level weather: Rain time: 73693 (now: false), thunder time: 47044 (now: false)
Level game mode: Game mode: survival (ID 0). Hardcore: false. Cheats: false
Stacktrace:
at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:636)
at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:334)
at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:547)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:427)
at net.minecraft.server.MinecraftServer$2.run(MinecraftServer.java:685)

-- System Details --
Details:
Minecraft Version: 1.7.10
Operating System: Windows 7 (amd64) version 6.1
Java Version: 1.8.0_60, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 1082966240 bytes (1032 MB) / 4080271360 bytes (3891 MB) up to 4080271360 bytes (3891 MB)
JVM Flags: 14 total; -Xmn2G -Xss4M -Xms4G -Xmx4G -XX:+UseLargePages -XX:+AggressiveOpts -XX:+UseFastAccessorMethods -XX:+OptimizeStringConcat -XX:+UseBiasedLocking -Xincgc -XX:MaxGCPauseMillis=10 -XX:SoftRefLRUPolicyMSPerMB=10000 -XX:+CMSParallelRemarkEnabled -XX:ParallelGCThreads=10
AABB Pool Size: 0 (0 bytes; 0 MB) allocated, 0 (0 bytes; 0 MB) used
IntCache: cache: 0, tcache: 59453, allocated: 0, tallocated: 5120
FML: MCP v9.05 FML v7.10.99.99 Minecraft Forge 10.13.4.1558 129 mods loaded, 129 mods active
States: 'U' = Unloaded 'L' = Loaded 'C' = Constructed 'H' = Pre-initialized 'I' = Initialized 'J' = Post-initialized 'A' = Available 'D' = Disabled 'E' = Errored
UCHIJAAAA mcp{9.05} Minecraft Coder Pack
UCHIJAAAA FML{7.10.99.99} Forge Mod Loader
UCHIJAAAA Forge{10.13.4.1558} Minecraft Forge
UCHIJAAAA AM2-Preloader{0.0.2} AMCore
UCHIJAAAA appliedenergistics2-core{rv2-stable-10} AppliedEnergistics2 Core
UCHIJAAAA CodeChickenCore{1.0.4.29} CodeChicken Core
UCHIJAAAA MCVanillaTweaks{1.0} Mariculture - Vanilla Tweaks
UCHIJAAAA WitchingGadgetsCore{1.1.9} Witching Gadgets Core
UCHIJAAAA OpenModsCore{0.8} OpenModsCore
UCHIJAAAA {000} CoFH ASM
UCHIJAAAA AnimationAPI{1.2.4} AnimationAPI
UCHIJAAAA arsmagica2{1.4.0.008} Ars Magica 2
UCHIJAAAA AncientWarfare{2.4.111-beta-MC1.7.10} Ancient Warfare Core
UCHIJAAAA CoFHCore{1.7.10R3.0.3} CoFH Core
UCHIJAAAA AncientWarfareAutomation{2.4.111-beta-MC1.7.10} Ancient Warfare Automation
UCHIJAAAA AncientWarfareNEIPlugin{2.4.111-beta-MC1.7.10} Ancient Warfare NEI Plugin
UCHIJAAAA AncientWarfareNpc{2.4.111-beta-MC1.7.10} Ancient Warfare NPCs
UCHIJAAAA AncientWarfareStructure{2.4.111-beta-MC1.7.10} Ancient Warfare Structures
UCHIJAAAA appliedenergistics2{rv2-stable-10} Applied Energistics 2
UCHIJAAAA aquaticabyss{1.1.1} Aquatic Abyss
UCHIJAAAA ATG{0.10.0} Alternate Terrain Generation
UCHIJAAAA MineFactoryReloaded{1.7.10R2.8.0} MineFactory Reloaded
UCHIJAAAA Baubles{1.0.1.10} Baubles
UCHIJAAAA Thaumcraft{4.2.3.5} Thaumcraft
UCHIJAAAA MineFactoryReloaded|CompatThaumcraft{1.7.10R2.8.0} MFR Compat: Thaumcraft
UCHIJAAAA Automagy{0.26.3} Automagy
UCHIJAAAA BiblioCraft{1.10.5} BiblioCraft
UCHIJAAAA BiomesOPlenty{2.1.0} Biomes O' Plenty
UCHIJAAAA BiblioWoodsBoP{1.9} BiblioWoods Biomes O'Plenty Edition
UCHIJAAAA Botania{r1.7-207} [Botania](Botania r1.7-207.jar)
UCHIJAAAA CarpentersBlocks{3.3.7} [Carpenter's Blocks](Carpenter's Blocks v3.3.7 - MC 1.7.10.jar)
UCHIJAAAA craftguide{1.6.8.2} CraftGuide
UCHIJAAAA customnpcs{1.7.10d} CustomNpcs
UCHIJAAAA props{2.0.2} Decocraft
UCHIJAAAA decorativemarble{Beta 1.1710.3} Decorative Marble
UCHIJAAAA decorativechimney{Beta 1.1710.3} Decorative Chimney
UCHIJAAAA diversity{ALPHA 1.6.1} Diversity
UCHIJAAAA MoCreatures{6.3.1} [DrZhark's Mo'Creatures Mod](DrZharks MoCreatures Mod v6.3.1.zip)
UCHIJAAAA Enchiridion{1.3} [Enchiridion](Enchiridion 2-1.7.10-2.0.2a.jar)
UCHIJAAAA Enchiridion2{2.0.2a} [Enchiridion 2](Enchiridion 2-1.7.10-2.0.2a.jar)
UCHIJAAAA EnhancedInventories{1.7.10-1.1.8} Enhanced Inventories
UCHIJAAAA ThermalFoundation{1.7.10R1.2.0} Thermal Foundation
UCHIJAAAA ThermalExpansion{1.7.10R4.0.3B1} Thermal Expansion
UCHIJAAAA enhancedportals{3.0.12} EnhancedPortals
UCHIJAAAA exoticbirds{1.0} [Exotic Birds](Exotic Birds 1.7.10 - 1.0.2c.jar)
UCHIJAAAA extracells{2.2.73} Extra Cells 2
UCHIJAAAA Forestry{3.6.3.20} Forestry for Minecraft
UCHIJAAAA ExtraFood{0.7.0} Extra Food
UCHIJAAAA ForbiddenMagic{1.7.10-0.57} [Forbidden Magic](Forbidden Magic-1.7.10-0.57.jar)
UCHIJAAAA NetherOres{1.7.10R2.3.0} Nether Ores
UCHIJAAAA redgear_core{2.2.1} Red Gear Core
UCHIJAAAA redgear_geocraft{2.4.4} Geocraft
UCHIJAAAA GraveStone{2.12.3} GraveStone
UCHIJAAAA GrimoireOfGaia{1.0.0} Grimoire of Gaia 3
UCHIJAAAA Growthcraft{2.2.2} Growthcraft
UCHIJAAAA Growthcraft|Cellar{2.2.2} Growthcraft Cellar
UCHIJAAAA Growthcraft|Apples{2.2.2} Growthcraft Apples
UCHIJAAAA Growthcraft|Bamboo{2.2.2} Growthcraft Bamboo
UCHIJAAAA Growthcraft|Bees{2.2.2} Growthcraft Bees
UCHIJAAAA Growthcraft|Grapes{2.2.2} Growthcraft Grapes
UCHIJAAAA Growthcraft|Hops{2.2.2} Growthcraft Hops
UCHIJAAAA Growthcraft|Rice{2.2.2} Growthcraft Rice
UCHIJAAAA HelpFixer{1.0.7} HelpFixer
UCHIJAAAA HopperDuctMod{1.3.2} Hopper Ducts
UCHIJAAAA mod_Invasion{1.1.2} Invasion
UCHIJAAAA JourneyMapServer{1.0.5_MC1.7.10} JourneyMapServer
UCHIJAAAA Railcraft{9.6.1.0} Railcraft
UCHIJAAAA MagicBees{1.7.10-2.3.3} Magic Bees
UCHIJAAAA malisiscore{1.7.10-0.12.7} MalisisCore
UCHIJAAAA malisisdoors{1.7.10-1.9.4} Malisis' Doors
UCHIJAAAA mam{1.7.10-1.0.2} Myths & Monsters Mod
UCHIJAAAA Mariculture{1.7.10-1.2.4.2a} Mariculture
UCHIJAAAA MariTech{1.0} Marine Technlogy
UCHIJAAAA MineFactoryReloaded|CompatAppliedEnergistics{1.7.10R2.8.0} MFR Compat: Applied Energistics
UCHIJAAAA MineFactoryReloaded|CompatAtum{1.7.10R2.8.0} MFR Compat: Atum
UCHIJAAAA MineFactoryReloaded|CompatBackTools{1.7.10R2.8.0} MFR Compat: BackTools
UCHIJAAAA MineFactoryReloaded|CompatBuildCraft{1.7.10R2.8.0} MFR Compat: BuildCraft
UCHIJAAAA MineFactoryReloaded|CompatChococraft{1.7.10R2.8.0} MFR Compat: Chococraft
UCHIJAAAA MineFactoryReloaded|CompatExtraBiomes{1.7.10R2.8.0} MFR Compat: ExtraBiomes
UCHIJAAAA MineFactoryReloaded|CompatForestry{1.7.10R2.8.0} MFR Compat: Forestry
UCHIJAAAA MineFactoryReloaded|CompatForgeMicroblock{1.7.10R2.8.0} MFR Compat: ForgeMicroblock
UCHIJAAAA MineFactoryReloaded|CompatIC2{1.7.10R2.8.0} MFR Compat: IC2
UCHIJAAAA MineFactoryReloaded|CompatMystcraft{1.7.10R2.8.0} MFR Compat: Mystcraft
UCHIJAAAA ForgeMultipart{1.2.0.345} Forge Multipart
UCHIJAAAA MrTJPCoreMod{1.1.0.31} MrTJPCore
UCHIJAAAA ProjRed|Core{4.7.0pre8.92} ProjectRed Core
UCHIJAAAA ProjRed|Exploration{4.7.0pre8.92} ProjectRed Exploration
UCHIJAAAA MineFactoryReloaded|CompatProjRed{1.7.10R2.8.0} MFR Compat ProjectRed
UCHIJAAAA MineFactoryReloaded|CompatRailcraft{1.7.10R2.8.0} MFR Compat: Railcraft
UCHIJAAAA MineFactoryReloaded|CompatSufficientBiomes{1.7.10R2.8.0} MFR Compat: Sufficient Biomes
UCHIJAAAA MineFactoryReloaded|CompatThermalExpansion{1.7.10R2.8.0} MFR Compat: Thermal Expansion
UCHIJAAAA MineFactoryReloaded|CompatTConstruct{1.7.10R2.8.0} MFR Compat: Tinkers' Construct
UCHIJAAAA TwilightForest{2.3.7} The Twilight Forest
UCHIJAAAA MineFactoryReloaded|CompatTwilightForest{1.7.10R2.8.0} MFR Compat: TwilightForest
UCHIJAAAA MineFactoryReloaded|CompatVanilla{1.7.10R2.8.0} MFR Compat: Vanilla
UCHIJAAAA me{1.3.2.1} More Enchantments
UCHIJAAAA AencEx{0.0.1} AencEx
UCHIJAAAA Morpheus{1.7.10-1.6.10} Morpheus
UCHIJAAAA numina{0.4.0.87} Numina
UCHIJAAAA OpenMods{0.8} OpenMods
UCHIJAAAA OpenBlocks{1.4.4} OpenBlocks
UCHIJAAAA PneumaticCraft{1.12.1-144} PneumaticCraft
UCHIJAAAA ProjRed|Transmission{4.7.0pre8.92} ProjectRed Transmission
UCHIJAAAA ProjRed|Compatibility{4.7.0pre8.92} ProjectRed Compatibility
UCHIJAAAA ProjRed|Integration{4.7.0pre8.92} ProjectRed Integration
UCHIJAAAA ProjRed|Fabrication{4.7.0pre8.92} ProjectRed Fabrication
UCHIJAAAA ProjRed|Illumination{4.7.0pre8.92} ProjectRed Illumination
UCHIJAAAA RedstoneArsenal{1.7.10R1.1.1} Redstone Arsenal
UCHIJAAAA Roguelike{1.3.6.3} Roguelike Dungeons
UCHIJAAAA StevesCarts{2.0.0.b18} Steve's Carts 2
UCHIJAAAA StorageDrawers{1.7.10-1.6.2} Storage Drawers
UCHIJAAAA StorageDrawersBop{1.7.10-1.0.3} Storage Drawers: Biomes O' Plenty Pack
UCHIJAAAA StorageDrawersForestry{1.7.10-1.0.5} Storage Drawers: Forestry Pack
UCHIJAAAA StorageDrawersMisc{1.7.10-1.0.1} Storage Drawers: Misc Pack
UCHIJAAAA UndergroundBiomes{0.7} Underground Biomes Constructs
UCHIJAAAA TaintedMagic{1.1.5.4} Tainted Magic
UCHIJAAAA ThaumcraftMobAspects{1.7.2-2A} Thaumcraft Mob Aspects
UCHIJAAAA ThaumicExploration{0.6.0} Thaumic Exploration
UCHIJAAAA ThermalDynamics{1.7.10R1.1.0} Thermal Dynamics
UCHIJAAAA TravellersGear{1.16.4} Traveller's Gear
UCHIJAAAA witchery{0.24.1} Witchery
UCHIJAAAA WitchingGadgets{1.1.9} Witching Gadgets
UCHIJAAAA WR-CBE|Core{1.4.1.9} WR-CBE Core
UCHIJAAAA WR-CBE|Addons{1.4.1.9} WR-CBE Addons
UCHIJAAAA WR-CBE|Logic{1.4.1.9} WR-CBE Logic
UCHIJAAAA craftingmanager{0.7.4} [Crafting Manager](zCraftingManager 0.7.5 mc1.7.10.zip)
UCHIJAAAA McMultipart{1.2.0.345} Minecraft Multipart Plugin
UCHIJAAAA JustAnotherSpawner{0.17.6} Just Another Spawner
UCHIJAAAA ForgeMicroblock{1.2.0.345} Forge Microblocks
OpenModsLib class transformers: [stencil_patches:ENABLED],[movement_callback:ENABLED],[map_gen_fix:FINISHED],[gl_capabilities_hook:ENABLED],[player_render_hook:ENABLED]
Class transformer null safety: all safe
CoFHCore: -[1.7.10]3.0.3-303
AE2 Version: stable rv2-stable-10 for Forge 10.13.2.1291
MineFactoryReloaded: -[1.7.10]2.8.0-104
ThermalFoundation: -[1.7.10]1.2.0-102
ThermalExpansion: -[1.7.10]4.0.3B1-218
NetherOres: -[1.7.10]2.3.0-12
RedstoneArsenal: -[1.7.10]1.1.1-89
ThermalDynamics: -[1.7.10]1.1.0-161
AE2 Integration: IC2:OFF, RotaryCraft:OFF, RC:ON, BC:OFF, RF:ON, RFItem:ON, MFR:ON, DSU:ON, FZ:OFF, FMP:ON, RB:OFF, CLApi:OFF, Waila:OFF, Mekanism:OFF, ImmibisMicroblocks:OFF, BetterStorage:OFF
Profiler Position: N/A (disabled)
Vec3 Pool Size: 0 (0 bytes; 0 MB) allocated, 0 (0 bytes; 0 MB) used
Player Count: 1 / 15; [EntityPlayerMP['Kharon_47'/3945, l='Wyldlans2', x=-1245.54, y=136.00, z=-14309.56]]
Is Modded: Definitely; Server brand changed to 'fml,forge'
Type: Dedicated Server (map_server.txt)