Units unloaded from a transport onto water usually get stuck and cannot be targeted by units. Seems to have something to do with water depth, but otherwise it seems altogether random. I know this isn't supported as a vanilla feature, but it would be nice if this bug got fixed :3
It actually is a vanilla feature, as you can transport naval fabbers with transports. I did have that happen to me once as well when I used an Astreaus to send a boat fabber to another planet with lots of water. It wouldn't build anything until I picked it up again and put it down in a new spot.