Every now and then a ship would get "lost" in the stack and when you try to create fleet with, say, two ships, it would come back without an error message but one of the ships will be a "size 1 fleet" and the other one will just sit there. At this point that extra ship that's not in the fleet can not be used in any other fleet.
Current workaround is to save, exit, and reload. it seem to be a ship list addressing problem.