Using MCA 3.6.1. I emptied my mod folder and left nothing but MCA, but it still crashed.

---- Minecraft Crash Report ----
// Hi. I'm Minecraft, and I'm a crashaholic.

Time: 4/20/14 9:38 PM
Description: Exception in server tick loop

java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(Unknown Source)
at java.util.HashMap$KeyIterator.next(Unknown Source)
at net.minecraft.entity.EntityTracker.func_72788_a(EntityTracker.java:259)
at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:680)
at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:587)
at net.minecraft.server.integrated.IntegratedServer.func_71217_p(IntegratedServer.java:129)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:484)
at net.minecraft.server.ThreadMinecraftServer.run(SourceFile:583)

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

-- System Details --
Details:
Minecraft Version: 1.6.4
Operating System: Windows 7 (amd64) version 6.1
Java Version: 1.7.0_51, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 194268104 bytes (185 MB) / 564133888 bytes (538 MB) up to 954728448 bytes (910 MB)
JVM Flags: 2 total; -XX:HeapDumpPath=MojangTricksIntelDriversForPerformance_javaw.exe_minecraft.exe.heapdump -Xmx1G
AABB Pool Size: 5205 (291480 bytes; 0 MB) allocated, 4727 (264712 bytes; 0 MB) used
Suspicious classes: FML and Forge are installed
IntCache: cache: 0, tcache: 0, allocated: 3, tallocated: 71
FML: MCP v8.11 FML v6.4.49.965 Minecraft Forge 9.11.1.965 4 mods loaded, 4 mods active
mcp{8.09} Minecraft Coder Pack Unloaded->Constructed->Pre-initialized->Initialized->Post-initialized->Available->Available->Available->Available
FML{6.4.49.965} Forge Mod Loader Unloaded->Constructed->Pre-initialized->Initialized->Post-initialized->Available->Available->Available->Available
Forge{9.11.1.965} Minecraft Forge Unloaded->Constructed->Pre-initialized->Initialized->Post-initialized->Available->Available->Available->Available
mca{3.6.1} [Minecraft Comes Alive](MCA-3.6.1 MC-1.6.4.zip) Unloaded->Constructed->Pre-initialized->Initialized->Post-initialized->Available->Available->Available->Available
Profiler Position: N/A (disabled)
Vec3 Pool Size: 3647 (204232 bytes; 0 MB) allocated, 2021 (113176 bytes; 0 MB) used
Player Count: 1 / 8; [EntityPlayerMP['LordBittmann'/374, l='Myst', x=250.68, y=63.23, z=28.15]]
Type: Integrated Server (map_client.txt)
Is Modded: Definitely; Client brand changed to 'fml,forge'

You would unfortunately have to remove all MCA villagers using MCEdit, or remove MCA completely, start the world, then replace MCA.

Note that 1.6.4 is no longer supported.