Might be a corrupted save, I don't know. I'm playing a slightly modded adventure game as a kobold, with a new race added. Pretty sure this bug has nothing to do with my mod, though, as the token sets are basically copied from humans, with cosmetic changes (language tokens, art mods, etc.).
I did 5 quests for one of my race's civs, 4 of which were killing the same guy. At one city, everything is normal, right up until I report my success at the capital. Then if I return, the resident spearmaster and the entire town tries to kill me. But the really bizarre thing is that the shopkeepers go hostile to everyone after spotting me. If I can successfully hide from them (or just get killed, and watch the aftermath), they quickly slaughter the rest of the town, if it was a skilled shopkeep.
The shopkeep insanity spreads to the rest of the civ if I attack anyone on my way out of town. But if I sneak out without incident, or just don't visit that one city, everyone else is totally normal.
Also, the group names in Legends mode show that I became a mercenary of, and an enemy of, completely different groups (up to 1 in each category for each town if I survive long enough to kill someone in each). If I report success in psycho-town before the capital, it ends up saying that I became an enemy of the entire civ (if I kill someone), yet in related entities I'm listed as a (member).
Or hm, on further testing, it seems that it's not limited to shopkeeps, they're just more noticable since they can each slaughter half the town. Anyone that goes hostile to me, also goes hostile to everyone else. Possibly because of my status as both a member and enemy of their civ (or before actually killing anyone, a member of the civ and an enemy of the one group).
Correction: anyone killing anyone makes me a member-enemy. Anyone attacking me becomes a member-enemy. Anyone attacking them becomes a member-enemy. I started a new game with this civ, and I'm still being attacked in crazytown, while everyone else rips each other apart. And now everyone in all the cities attacks me. The ability for creatures to simultaneously be a member and an enemy of a civ results in something very much like contagious insanity.
Digging deeper in Legends, it appears that "former member" status works for PCs. NPCs retain their civ membership, but become enemies of their own individual city group. Same effect still, a highly contagious "rage virus."