Federation fleets have one terrible game damaging BUG... when you open Fleet manager of Federation fleet and you press to replace/retrofit some ship design to another ship model you are presented only with list of your own "Player" ship designs, not with the ship designs from Federation ship designer.
meaning if your Player Battleships are named "BS1", "BS2", and Federation autodesigner battleship is named F1, and you design your own version of federation battleship F2 in fed ship designer... now open your main Federation fleet managere, click the retrofit button on F1 ships.. you will be presented with BS1, BS2, but not F2. If you choose BS1 or BS2, it will simply turn the "upgrade"marker on the fed fleet on.. and when you send it to the shipyard, it will simply get stuck at 0% all the time... You are unable to cancel the retrofit to BS1/BS2, because you are unable to choose any ship from federation list... When you get stuck like this, The only way to disband these nonpgrradeable/stuck Federation ships and spend tons of resources for rebuilding.
I think this has been posted long time ago, and still has not been fixed.