In the pictures below the map shows a village and a nether fortress that are actually not in the world.

Minecraft: 1.10.2
Version: antiqueatlas-1.9.4-4.4.5
Forge: 12.18.3.2316

See full list of mods below (LordDan's Banished 2 modpack, plus upgraded forge and some mods)

'[MC 1.10.X] BetterCombatMod 1.4.jar'
1.10.2-ExpandedIndustry-1.1.0b.jar
1.10.2-HardLib-v1b.jar
agricraft-2.0.0-0.10.0-a18.jar
animania-1.10.2-1.1.5.jar
antiqueatlas-1.9.4-4.4.5.jar
AppleCore-mc1.10.2-2.2.0.jar
AppleSkin-mc1.10.2-1.0.5.jar
'Better With Mods-0.14.24-1.10.2.jar'
betterbeginnings-MC1.10.2-b0.9.8-R6d.jar
BetterFps-1.4.5-1.10.jar
boatifull-0.4.0.jar
Chameleon-1.10.2-2.3.0.jar
'Claycraftmod v3.0 - MC1.10.2 Forge.jar'
compatlayer-1.10-0.2.9.jar
CoralReef-1.2.jar
CraftTweaker-1.10.2-3.0.26.jar
'Customized Dungeon Loot 1.10.2 (v.1.0.1).jar'
'CustomMobSpawner 3.10.1.jar'
dropanything-1.10.2-0.0.1.jar
"DrZhark's Mo'Creatures Mod-10.0.6.jar"
DynamicSurroundings-1.10.2-3.4.5.6.jar
EnderZoo-1.10-1.2.3.44.jar
Farseek-1.9.4-2.1.jar
FastLeafDecay-v11.jar
FatSteve-alpha-0.0.4.jar
finite-water-control-1.10.2-1.0.jar
FriendlyFire-1.10.2-1.3.0.jar
h3ntlibs
HardcoreDarkness-MC1.10.2-1.9.jar
hardcoreore-1.10.2-0.0.32.jar
HardModeTweaks-1.10-1.2.2.jar
HungerOverhaul-1.10.2-1.1.0.jenkins118.jar
Hwyla-1.8.17-B31_1.10.2.jar
incontrol-3.5.5.jar
infinitylib-0.10.0.jar
itlt-1.10-1.0.0.jar
jei_1.10.2-3.14.7.420.jar
LunatriusCore-1.10.2-1.1.2.38-universal.jar
materialchanger1.0-1.10.2.jar
MCA-1.10.2-5.2.3-universal.jar
mobends-0.22.5_for_MC-1.10.2.jar
MTLib-1.0.3.jar
MultiMine-1.10.2.zip
NewWorldOrder-1.10.2-1.0.0.jar
PotionCore-1.5.2_for_1.10.2.jar
PrimalCore-0.2.39.jar
QualityTools-1.0.4_for_1.10.2.jar
RadixCore-1.10.2-2.1.3-universal.jar
RealisticItemDrops-1.0.9.jar
RTG-1.10.2-4.2.0.0-snapshot-3.jar
signpost-1.10.2-1.05.5.jar
simplebarrels-1.26e.jar
simplebedding-1.0.0.jar
simulatednights-1.11.2-1.2.0.jar
SoundFilters-0.9_for_1.9.4.jar
special_ai-1.10.2-1.1.3.jar
SpiceOfLife-mc1.9.4-1.3.8.jar
Stackie-1.10.2-1.6.0.44-universal.jar
'Stellar API-0.5.4.1.4.jar'
'Stellar Sky-0.5.5.1.9.jar'
stg-1.0.2.jar
StorageDrawers-1.10.2-3.7.9.jar
Streams-1.9.4-0.3.jar
structpro-3.8-1.10.2.jar
Survivalist-1.10.2-1.10.1.jar
ThingsThatMatta-1.10.2-r1.jar
ThirstyBottles-1.10.2-1.0.1.0.jar
Timberjack_1.10.2-1.5.jar
ToughAsNails-1.9.4-1.1.1.21-universal.jar
UndergroundOcean-1.1.0_develop_a69b2f0_alpha.jar
'VisibleArmorSlots[1.10.2]-2.1-legacy.jar'
WearableBackpacks-1.10.2-1.7.0.jar
wolfarmor-1.4.1.0.jar
WTF-Expedition-Gameplay_1.10.2_v-1.1.jar
WTF-Expedition-WorldGen_1.10.2_-v1.5.1.jar

As the structure detection code changed with contemporary Minecraft versions, this is obsolete and I believe this should not happen with the current code. So I'm closing it.

interesting...

As it happens, TehNut has a pull request for a structure watching rewrite. I'm not sure, but that might be just what the doctor ordered.

in the meantime, you might be able to mitigate the damage by setting autoVillageMarkers to false in the config

The logic in my PR is identical to the live code. It's just a proper API now. The logic pulls the data from the world data, though. Not sure why these invalid structures are appearing.

I'll take a look at possibly cleaning up the logic and adjusting my PR accordingly.

Thanks. What does autoVillageMarkers=false do for me?

Come to think of it, nothing. Nevermind that, it would just get rid of the marker.

Speaking of which, does the marker appear above the non-existant villages?

no, it does not.