I have been reading a lot of the post and have noticed a possible common cause of some of the issues.

I have noticed that the quick save was bleeding over information from the last game saved on it.

Note: Going to leave out the specifics so as not to spoil anything.

For example: When you first talk to the wizard at the gates in the beginning of the game he may have a response to a quest you haven't started yet.

I haven't tried it with the new patch yet but, was able to reproduce the effect by saving a game with quick save, then starting a new game and using the quick save.

Temporary fix is simple, just deleted your quick save game before saving a new game to it.