You might be overloading the boat. Animals count as pawns. So if you are say loading two human colonists onto a rowboat, and then add an animal also it'll let you do it, but once you exit the map they will be gone, that happing will also mess up something within which will make it impossible to use the boat.

it might be a problem with the experimental version and this too. I'm having it with one man in a rowboat, if I try to send them on a quest

i was doing it in a caravel