Two bugs I'd like to point out that I've personally found annoying:
Kill Shot - the range on this shot is different to other hunter shots. I've personally macroed Kill Shot and Arcane Shot on the same button to level with, and it's been rather irritating to have to move back to fire Kill Shot when Arcane fires just fine.
Automatic mob targetting - when a mob dies, you automatically target a different mob nearby. This annoys me because if I'm spamming a shot (Kill Shot, for instance) to finish off a mob, sometimes the mob I'm hitting will die and I'll hit another mob by mistake... or my pet will start charging towards some other mob that I don't want to pull.
Adding to these is of course the Volley bug that people have been complaining about for awhile, where your ranged weapon loses excessive durability when casting Volley.
I hope Blizzard fixes the Auto-mob target issue before I start raiding.... I can see some wipes happening with that one. The others I can live with unless the raids turn out like Hyjal - I might have to start carrying a spare bow again!