If you hold spacebar to jump on a boat you accumulate a lot of fall damage which will all be given at once when you either: jump off of the boat onto ground or when you let go of space bar, which probably gives you fall damage from standing on the boat (water particles will appear because the game thinks you fell on water).

Because my description is a tad bit confusing I made a video showcasing the bug: 

https://www.youtube.com/watch?v=W-kbYgSq4MM

This is my idea on why this happens:

The boat lets you jump before actually standing on it (boat collision has always been a bit awkward) so you don't actually land before jumping again, meaning you stay in the air as long as you hold jump / space. This also explains that when you jump on a boat you slowly fall down for a brief second and then take fall damage (if you fall from enough distance / perform the bug).

This is just speculation though, I'm not a game designer and have no idea how the engine works so take it with a grain of salt.