I'm having the same problem with a bonus quest on Tatooine called "Burn it Out". When I was doing the quest I actually killed all the Palowa it told me too along with the infected ones and the leader at the back of the cave, however none of it except 1 kill was registered. After the first kill was registered the bonus quest dissapeared from my log and I finished the main quest series. Now I can no longer get inside the cave to kill them and after logging back in the bonus quest now appears. This bonus quest can't be abandoned or reset and is now stuck in my log permanently as I am no longer allowed back in the cave after finishing the main quest.
Having the same issue with the quest, "Migraine" a bonus quest for a non-repeatable in the Nar Shaddaa Bonus Series. The quest was completed and randomly popped up in my quest log when I was questing in Alderaan.