Thought I'd pitch in my own list of 'bugs and fun' I've encountered in 3.C version.
~ Archeologist building. Using the excavate stone function is supposed to create fossils, chests, and other oddities at a low chance. These created chests, relics, fossils, etc, are NOT openable/usable. I have around 80 of these in my stockpile, and all reactions are unusable in the arch-building, and are sitting in my gem stockpile. Naturally dug up ones, work perfectly fine and get auto-queued to be 'opened' - only ones created by the 'excavate stone' reaction seem to be broken.
~ Giant Elephants. These are a randomly generated variation of animals I found roaming my embark recently... do you think elephants are scary? if My calculations are right, giant elephants are upwards of 41,000,000 size. ._.; but yes. After capturing, taming, etc one - I tried to run the 'armoring' process on one, to my despair, it didn't work. Promptly, I died due to a hilarious incident with a pillar, and a roof that spanned the map... so I didn't get to retest it a couple dozen times.
Last I recall, it was mentioned giant versions of animals should be armorable, but they appear to not be so. (though giant elephants in steel armor sounds a smidge overpowered...).
~ I noticed another very odd glitch, with the religious tier 3 building, and sacrificing a life. I had a necromancer I couldn't cure for some reason (probably as it's not an 'affliction' and won't cure it), so I decided to make him useful and sacrifice him to armok!... except... he didn't die. And continued to spawn 'bloody battle axes' or similar, constantly to the point I had to just stop him before I had 100 of these darn things! I've been trying to rebuild my fort (similar time with the elephant incident -.-;) to retest it, but it may be because he's one of the 'cursed' castes, or perhaps a genuine bug? Can others chime in on their experience? (probably posted, but trying to detailed ALL bugs I see).
~Gnome Sieges. I can confirm pretty much after they lost 2 outpost liason's, the next 'visit' of gnomes was them riding war animals called 'blow gunners' - yet using freakin' steel rifles. quite hilarious picturing a midget on a war tiger, at least. But last I read - they aren't supposed to siege you, and especially not so easily after only 1-2 loses of a outpost liason (they just LOVE spawning on goblin ambushes >.>).
~ More of a vanilla bug, but one I thought I'd bring up here in case it's fixable from dfhack now. But yes. I've noted over many maps, if traders lose their wares via them being eaten, the building being forbidden or destroyed by accident events but generally, the merchants are unharmed/touched, there's pretty much NO 'anger' for the lose, vs you 'trying to rob them' in the trade menu or similarly just murdering them. This means generally trying to lead their animals into 'accidents' or if you're a dirty cheat, forbid/break down the trade depot, they'll leave everything they brought on the floor and walk off happy as could be with no malicious 'demerit' that could spark a war with them. I tested this with elves for at least 15 years solid, and never had an issue, the trader was always neutral to happy each time, and all I did was deconstruct the trade depot - and they left without me paying a dime. Feels kind of... flimsy. You can argue 'don't do that then!' - but speaking from natural deaths or accidents too. Perhaps some way to count the value they enter the map with, and exit with, and if it doesn't add up (as you have to trade an equal or greater value to get them to trade anything, meaning they should leave at exactly their entry total, or more) - you could cause such dirty tricks to be avoided and cause wars/them to not return if you do. Not 'game breaking' unless you exploit it, of course. But I thought noting it as it could be a simple fix (if Meph can do such a process to check value on entry/exit) it was worth a note.
~ More to come as I find them! I'll edit and update this post to keep it tidy and simple.