I know it happens because I remember a change I made only for Shy. She might have moved and fall off the edge of a room.
Another thing that has happened a few times and only in Asylum: sometimes in the hallway with the lights puzzle when I try to leave, the player character disappears and it doesn't actually move back to the other hallway. I can still run around and the camera follows but I can't leave the lights puzzle hallway and my player character has completely disappeared.
The only way to get out is to close the game.