I'm on Stadia, had the same issue where it skipped the exit naut ship cutscene, then clicking the clam seems to make the game unresponsive beyond wandering around.
To fix, I started again from before the battle to exit the ship. Rather than fight it out, I rushed the ship controls, activated, and it triggered the exit cutscenes. I've been happily playing for many hours since.
I've encountered a few other game breaking bugs but there's always been a way forward. Careful with your save games. Good luck.
