When a ship changes direction, troops crawling on it's exterior do not move with it, instead teleporting from the ship's front to it's rear or vice versa. If there is no ship under them anymore, this causes them to fall off.
Kinda related, and a bit uncertain about this, but when you capture a ship if there are any guards left they will start fighting the crew. Not sure if this is a bug or if that's just how boarding works, but it's kind of weird. It would make sense if crew just surrendered once the bridge fell, instead of switching sides.
Ah yes, that should probably not happen. It's now on the list for v7.2.2.
The 2nd thing is intentional, though.