-Bodies aren't decomposing. I'll get the miasma if they're underground, but when it clears, the remains don't convert to usable bones. I've got 15 dwarf bodies littering my fortress, waiting for when I finally build my cemetery and they've been there for a year or so. Creature bodies aren't rotting either. All my corpses look freshly killed and claim to be "Urist McDead's skeleton", but when I try to make bone items, I get "Urist McConfused cancels Make bone bolts: Needs unrotten bone body part".
-My outdoor refuse pile isn't emptying at all. It's getting pretty full of vermin remains and turtle shells. I also cannot find bone or shell on the stockpile list in order to sequester them away in a separate stockpile for future use like I normally do. My dwarves also aren't hauling animal "skeletons" there.
-I had a war dog come in in a migration, but before it even got out of new-migrant-mode, I got the message "War Dog has been struck down!". There was nothing anywhere close to the body that could have killed it.
-I lost my starting miners, and for whatever reason, everyone refuses to use the pick that one of them left behind. The other one's in use, but that may be because the miner that originally had it went berserk rather than insane and it was war spoils or something. I've got multiple people with mining designated, but the pick's just sitting in the stockpile, looking perfectly usable.
-I love using the "kill" feature in the new squad system, but when the target dies, the order sticks around. My squad will just stand around the body with "Kill Urist McAlreadydead" as their job until I manually cancel it.
-When my soldiers die, they aren't automatically removed from their squad listing. And there isn't even any zoom function on that screen for me to easily check if they're dead. I have to occasionally remake the squad just to get rid of the ghosts in the lists. I could theoretically just check off the names against the deceased list, but that's far too tedious.
-I constructed a wall, and one of the pieces of it got stuck mid-building. It was just saying "Waiting for Mason", and even appeared to be an active job, though no one was doing it. Suspending it didn't clear it at all, nor even drop it to inactive again. The surrounding walls were constructed during a time when I had a lot of people going crazy, so that may be related. I had to cancel the construction completely and redesignate in order for it to get built. EDIT: I found the stone that was related to the original wall. It was marked as forbidden. I've forbidden stones in the past for walls, and they'd go pick up a new one, but not now.
-I lost my expedition leader a few months back and there's no new one yet. The position's gone from my Nobles list, so either it's a bug or the dwarves are now really slow about getting around to elections. EDIT: When I finally remembered to make them stop trying to kill an already dead goblin thief, one of my soldiers turned out to be the mayor and all of a sudden the mayor position appeared on my noble's list. As did captain of the guard, for whatever reason. I hadn't seen the announcement at all, nor had I any migrants coming in to trigger the next level.
-Other things: my hunters aren't hunting, I had to irrigate to get underground crops, my migrants often have skills that they don't have the job activated for and it is a pain having to check all of them to catch that, and I had to switch back to space for closing screens so I wouldn't be driven crazy by having to hit the ESC key so freaking often.