This linked video should make things clear enough:
http://www.youtube.com/watch?v=o5LdYDlUink&feature=youtu.be

As you can see, when you watch a player ride a boat in multiplayer, the player sometimes seems to "jump" to a position outside the boat, leaving an empty boat. This happens REGARDLESS of the distance between the players, and wether the boat is moving or not. I have tried this on different worlds, still happens.

Note that the player himself is able to ride the boat normally, and the boat itself acts as usual. It is just the player riding it that, when viewed by other players, seems to jump and disappear.

It is easy to reproduce: Just start up a multiplayer world, and watch someone ride a boat!

UPDATE: The same bug occurs when riding a minecart.