How to replicate:

1. place a command block which is constantly executing "/tp @e[type=Boat,c=1] ~1 ~ ~"
2. summon any boat
3. get in
4. type "/tp @e[type=Boat,c=1] ~1 ~ ~" in chat

You'll notice the command block isn't allowed to interact with the boat when a player is riding it, however, the player inside the boat is allowed to manipulate the boat by using the chat (/tp @e[type=Boat,c=1] ~1 ~ ~) . Executing a command as the player inside the boat (/execute <player in the boat> ~ ~ ~ /tp @e[type=Boat,c=1] ~1 ~ ~) doesn't work either. The same effect applies to /entitydata @e[type=Boat,c=1]

Causing a bit of lag by taking a screenshot sometimes results in the boat being teleported as long as the game is lagging