Yea well known problem. Happened to me last game but I was lucky that it happened much later so I was able to finish the game without needing to go inside the ship any more. Definitely not intended and when I looked for answers a few days ago there seemed to be no information.
Have you tried the latest patches already? I was hoping the huge patch would have fixed this.
my game is up to date with stream so broken save not that cool consider i spend 14 hours on it
