So what happens when you use boarder troops to capture a ship and immediately retreat? You run away in a very masculine manner with the ship in tow.
Problem is, the ship has to go somewhere. You need to choose a certain place to go to.
Now what happens if you take a landship, retreat with it, and find that there are no roads connected to said city?
My personal, and completely ignorant, advice would be to choose an option to abandon the ships, either destroying them or giving them up to the enemy
Now that is indeed a very good point, and one which I missed at the time! I've added it to things to be fixed.