How to reproduce:
1. Get a (skeleton) horse in a boat as a passenger
2. Get out of the boat
3. Now there is no way to get the horse out without killing it

If you press F3+B you can clearly see the bounding box of the boat is completely enveloped by the bounding box of the horse, making it impossible to hit the boat. Since in 1.9 boats can only be broken by hitting it, there is no way to get the horse out without killing it.