The Trade wagon displays as a 3x3 tiles, but in actuallity it only occuplies a 1 tile space. What you're seeing is probably the wagon overlapping onto the water.
There's an issue in 1.2.5 where pathing can ignore structures in some edge cases. I have a fix in 1.3, but I could release it early if it really bugs you.
Edit: Masklings shouldn't ignore the walls, so don't worry about your defenses being useless.