Plot hole: When Morgan and her Slave/New Boyfriend are escaping from the burning ship, which is going to explode any second, they emerge onto the deck, run up a flight of stairs, cross the deck to the stern rail, look about themselves, then dive overboard. They know the ship is about to explode and are desperate to get overboard. The railings are about a metre away from the hatch they emerge from in the first place - why not just jump overboard there?
Plot hole: When Injun Joe is about to kill Huck, Tom takes notice of the chest full of gold coins and then empties the chest out (offscreen) because it was too heavy for him to lift, and then tricks Injun Joe into trying to retrieve the empty chest, resulting in Injun Joe falling to his death. The amount of time that passes between Tom glancing at the chest and then tricking Injun Joe before he can kill Huck is roughly 5 seconds. There's no way Tom could have emptied out of the chest in that little amount of time if the chest was too heavy for him to lift in the first place, especially without making a sound.