Understand that the term 'docking' does not mean that a ship actually pulls up to a dock and ties up. Sometimes it just means they anchor in the immediate area. If you anchored within the harbor, they you 'docked.' You sure were not underway.
Hate to tell you but ships don't have to be "docked" to a wharf to get fuel or supplies transfered to them. Even if you're anchored offshore you can have suplies and fuel brought to you. Also ships regularly dock besides each other where one ship docks to the port, the next ship to the ship docked to the port and so on.
I still say that before "enhancements" are made that the bugs that exist in the game should be fixed first. This issue isn't a bug so in my opinion should take a back seat to real bugs such as the leader bug. Work on the known bugs without introducing any new "enhancement" code into the scenario and get a stable and bullet-proof game.