What exactly do you mean by 100%? RPG's tend to be made so you can't do 'everything' in one single run-through, from side-quests, having to choose who you focus on NPC-wise, DS/LS, etc. Tho I think in Kotor2 you could do a large majority if you plan it out well, but that takes foreknowledge.
If you missed some quests from not doing them 'in time' then they're out of reach (except maybe via the save game editor, not sure). I think the quest log is supposed to take them off but it doesn't. I remember some contention about a couple other quests like that. They're just side-quests tho, not important to the main plot or anything.
P.S. Welcome to the forums.