I've run into 2 significant things in my play through:
1. After saving Stingtail from the assassin I can only talk to him with Ifan. For everyone else he'll stand up and a dialogue box will appear for a quarter-second before it automatically closes and he lies back down.
2. I dismissed Lohse to play with Sebille for a while; now Lohse seems to have completely disappeared. She no longer appears where she was recruited in the Fort Joy. This was after escaping the Fort so I'm not sure if she was murdered by hostile guards on the way back, but I haven't found her body.
