The list is long. Alot of problems with doors, scripted sequences, and enemies that chase forever. And double spawning waves. I was doing the hunter stuff and it decided it would be peachy to throw 5 regulars and 2 bosses at me in one wave, probably because I was stuck behind the door where they are supposed to spawn.
I ran and they chased me through this entire ship, full of friendly stuff to me, all of which is blasting away at it. Created this huge pile of path-confused stuff all blasting in 100 directions, was hilarious. I eventually went down, and revived nearby with the stealthy medic probe thing and as soon as I spawn one of the bosses flies over and nails me, ignoring the stealth. When I did eventually beat that mess, the script froze me in the ... stage forever.
I get to the final boss of a certain planet and I can't target it. I ran around for a bit and spammed ae stuff but yea didn't work. When I eventually did get to fight it, it would do fun stuff like an area stun. I'd stun it before hand, my stun wouldn't work, his would, but it would burn MY cooldown.
Had an entire instance get sort of frozen in time. Dramatic music is playing but nobody is fighting and everyone is marked friendly.
Seems like the difficulty of the last few quests sort of assumes you are bringing a friend. I have to have top gear and the right companion and lots of luck to take on multiple bosses, and they seem to throw them around like candy. If they are going to spring that crap on you the mobs shouldn't chase forever. And not being able to use an elevator or other item because you are "in combat" is really stupid.
The most annoying thing of all out of everything is traveling to objectives. If you ever go towards something as the crow flies, inevitably it is at the top of a cliff. A cliff with one entrance, 30 miles back in the other direction through hordes of annoying trash. Or on corellia you get to fight or fly through annoying tunnels trying to figure out which actually leads to the map icon.
I remember being extremely annoyed at something when I was doing the knight stuff, but I can't remember what it was.