Scurrin

Found a way to fix this: Just have to take all the stolen items and drop them in a chest. Then have your follower pick them back up again which will switch the flag.

I am having this exact issue and have seen a few others post it. It seems to have something to do with having a companion pick up items in a container. Not sure if it puts them over their weight limit and it just flags everything as stolen. EDIT: Just taking the stolen items dropping them into a box and having your companion pick them up will switch the stolen flag back. So yeah, who needs fences anymore?