Carthaginian Coton holds 5 ships. But if there are units on board, they count each as a whole ship. Could you let the ships go into Coton for repairs, along with the units on board?
This series of errors arose when my ally and I simultaneously began the construction of our own city center.
My (blue) city center was completed early. He had only a construction site (red) that fell under my borders. (The Dodecanes map)