Many NPCs don't seem to realize certain things have happened. In particular:
Commander Clyver's dialogue is exactly the same after returning to Defiance Bay in Act III, which makes very little sense. He was explaining to me what a Crucible Knight is and that sort of thing. I supported the Crucible Knights in Act II, and given that fact and what happened at the end of Act II, you would think his dialogue would be different.
Also, I went back to Heritage Hill for a bounty (also in Act III) and one of the guards outside talked to me as if I had never fixed Heritage Hill. Talking about unnatural noises that started months ago and that sort of thing.