I experienced the same stuttering too midgame, a few things that leap out at me was that i had a hospitalised bar brawler with active furnace jobs on repeat (burning wood) never actually cancelled while they were waiting in a hospital bed but were taken up by someone else when i assigned them the wood burner labour to cover the hospitalised person's shift (mangled floating ribs before any healthcare was put in place).
The diagnostian also refused to see them under the notion they weren't 'resting' when they were clearly in bed recieving food, i would submit a save as per usual but the game was modded and probably wouldn't be very conclusive, hopefully these will give people a bit more of a idea for a testing condition to try as it started lagging with not a lot of people or game items in play, most definitely could be something else though.
Ha ha, interesting. I have the same-civ restriction on most of it, but the site takeover code doesn't have that (peaceful or otherwise), when they are searching for a market. I suppose the question is why a bandit gang was searching for a legitimate market site, rather than a target market site. There will clearly be growing pains, but it might align well enough with the future villain stuff as we get going here -- the elves would be a problem rather than a subordinate site.
I think this may also be related to how kobolds hiding in gang/villian/refugee areas like catacombs out of the way of conflict and not involved in site defence implicitly take over a site by being the last remaining sentients after a massacre without a raze, the band of elves for whatever reason migrated out and being the only occupants the site now belonged to them. Happens in other minor landmarks too, fleeing civ members running from sieges sometimes turn up in places like civ-leader tombs if they're out in the wilderness just hiding (i had one return to my fortress as a migrant much later).
Yet to try extorting a necromancer tower though or assigning overseers to it in the hopes it wouldn't crash as a example, but acting wierd most definitely as probably expected with non-defined civs.