A lot of them seem to be related to doing them the wrong way around which is quite easy when you use the teleportation gloves liberally I think, and also if you use thievery a lot.
For example the Beast quest line can bug out a bit if you steal the key from the guy in the arena before you talk to him. If you place it back in his inventory later but have already opened the door for that key, you then can't progress past the bit which says you need to find a fitting door.
Red Prince's quest marker at least also has issues if you agree to meet the lizard, throw Prince out of the party, kill Lizard with Sebille and then pick up Prince again later. The dialogue accounts properly for the action, but doesn't update his quest or the map marker.
Imprisoned Elf I can confirm I received rewards from BOTH Amyro and Saheila but quest still won't close.
The Arena of Fort Foy doesn't close after beating the battle. Have the option to fight against a companion but can't then select one.
Withermore Soul Jar remains open saying I destroyed the jar and he is free.
