Things I recall being faction bugged (Sing along if you know the words)

[Grouch]

Lesser magic eaters and Medium magic eaters kill each other, I feel all magic eaters should get along and wreck parties who decide to cast spells in the appropriate places.

Spiders kill each other if their type is different

Gnoll random gnolls and cave prowlers kill each other

Sometimes enemies in Breadblood (I think ghouls?) Will kill other spawns

Things step on their own traps and get hurt (The trap faction and the trap layer faction are at war, very messy)

There is probably more, but I forget feel free to pitch in.

[LawfulStupid]

There are a lot of seemingly friendly things in The Grand Fissure, like the giant ticks. Can also confirm Breadbloods, that gets out of hand when they get faction bugged because the summoners just start popping off when you're miles away.