I'm having this issue as well. I sailed to a different island in a large ship and tamed a horse. I was able to get the horse to jump on the ship but when I tried to sail back home, the horse stayed stationary while the ship started to move. When the horse hit the back of the ship, the ship stopped and was unable to move forward. I could however sail backwards until the horse hit the front of the ship.
Thanks!
Oh and by the way, I'm LOVING this game!!