I would recommend everyone staying away from the dungeons in Caed Nua / Stronghold. You can finish the main quests, but it seems that if you go deep enough into the dungeons after, it'll trigger this issue no matter what.
I ended up leaving the area after finishing the main quest there and traveling south to the main city in Defiance Bay. I'll tool around there for now till they fix this damn bug. I have 3 people in my party with companion animals so it makes it unplayable when the bug occurs.