I've also had the same problem with vanishing characters in cut scenes. Here's a few other problems I've been having:
- Breakable objects permanently stop dropping items after returning from Canada and leaving the game. On my first play through, this didn't happen until after beating the final boss.
- The Chinpokomon "Shoe" does not appear in the final area. I looked up a video to find its location, but it does not appear there when I play.
- Some cut scenes suffer audio desync. Usually dialogue is triggered as each character speaks, but other sounds are trigger long before the event is shown.
- On one occasion, the first cut scene for the Abortion Clinic stopped while my character was taking a photo of the clinic records. Other sounds continued except for character dialogue, but the video froze and I had to skip that scene entirely.