Where does your boat start when your mission begins? If your boat begins on the beach with the units in the boat, then I think the boat might try to find what the AI feels is an ideal landing spot.
For example, I have a mission where an AI boat starts about 300 meters out and drops off an AI soldier on the shore, but the boat lands about 50-100 meters away from where the waypoint is located in the editor. I don't know how to make the boat land exactly where the waypoint is. I'm going to guess that if I made the boat start at the beach already, it might move out, find a "good" spot, and land.