When you are piloting a ship, your character shuffles around the ship, if you don't have anything blocking you from falling off the sides of your ship you will fall into the water.
I made a galleon style ship with the wheel on the top deck and my character ended up on the bottom deck of the ship after sailing around a short time.
I have tried to block my player in place but there are times it will still slip through the barricade I try make no matter the material.