In no particular order…
The Maw of the Void ‘secret’ in Darkshore is not working correctly, when you jump in the vortex you get the cutscene to get sucked into the middle and the screen fades to black, but then it just comes back with you still in the pool, instead of getting ported to the secret area as your supposed to, making the achievement related to it impossible to complete.
The quest Lawn of the Dead in Alterac (the one that rewards the singing sunflower pet) is bugged and impossible to complete as Warden Stillwater just simply doesn’t spawn, even though you get the emit about needing to kill him quickly before you are overwhelmed.
The childrens week quest from Stormwind to take your orphan to a chopper ride in Westfall does not give you credit for completing it, making the quest chain impossible to complete.
Some low level dungeons are missing from dungeon finder, at least Deadmines and Gnomeregan that I have seen so far. The Deadmines quest chain also doesn’t work properly as the quest to kill Helix (or any of the parts after that) does not auto complete and give you the next part as it’s supposed to, making you have to run all the way to the start to hand in and pick up next part after every boss.
I had really bizarre flight path bug, where I was taking flight path from Ironforge to Aerie Peak (I did not have Menethil Harbor flight path, which I feel is what caused the issue), where first it did a weird loop around Menethil with really jarring direction change, then flew to Aerie Peak, but instead of landing, did a loop around Aerie Peak and started heading back, flying directly through a mountain, and going all the way back to Menethil, then looped around again, and then finally actually flew me to Aerie Peak.
The announcements you get from leveling up are bugged, first every time I level-up it tells me I reached level 0, and it also tells me I got a talent point every level, even though I actually only get them (correctly) every odd level. And the talent button keeps flashing like I would have unspent talent point every time I get one of those levels where I don’t get one.
Some dungeon quests don’t give guild reputation at all. Stockades ones at least didn’t.