I haven't looked at the mission but probably yes. You sometimes get odd behaviour when the game can't quite figure out how to do what you have told it to do. The interference is not always obvious: for example an object placed too close to a road may make a lorry a mile away down the road drive in a funny zigzag.
Whenever you have something that doesn't work, and you can't figure out why, it's often a good idea to create a copy of your mission and delete eveything except, in this case, the boat. See if it works then. If it does, add things back till you discover the problem.