When you make a new fleet, and choose "Add a new ship to this fleet", you can choose any of your ships, no matter what port they are in. HOWEVER: If a fleet becomes empty for some reason (all ships sunk, stolen or removed), the fleet belongs to a port, and you can ONLY add ships from that port to the fleet. If you want to make a fleet with ships from another port, you'll have to first delete that fleet (even if you have plenty of admirals), then make a new fleet. I find this rather cumbersome (yes, I do this a lot).
Suggestion A: When adding ships to an empty fleet, you can ALWAYS choose any ship from any port.
Also, the list of ships to choose from can be rather cumbersome to look through if you have lots of ships not in fleets.
Suggestion B: When adding ships to fleets, the list of ships should be sorted according to which port they are in.