The workaround I always used to SM add fuel to a ship was to use the F12 'Task Groups' window, transfer a tanker or fuel harvester to the fleet with the stuck ship, hit the 'Equalize Fuel' button, and then transfer it back to its original fleet. If necessary, transfer it to a fleet at a colony world to fill its tanks first.
The only way to flat out add fuel to an empire is to use the 'SM Mods' button on the F2 'Population & Production' window to add fuel stocks to a colony.