I'm pretty sure a couple of them don't flag as being completed even though they are. I've completed a bunch of quests like I would have in the alpha, but half of them aren't removed from the quest log.
As far as this part of the conversation goes, I've run into this as well. There are several quests I know I'm done with, but aren't clearing past the last step. I'm not sure if it's me or the game right now.
