If you prep a ship and get a message stating it's crewed but more fuel is needed, that particular ship is stuck there until you produce or add more fuel to the planet's reserves. You don't want the Starbase to run low or out as the craft you buy that require fuels will be trapped there, greatly slowing you efforts to build and expand. It might be advisable to establish one or more Mining Stations on the Starbase to prevent this. Should you attempt to navigate a craft between worlds and receive a message saying the trip requires more fuel to complete, you'll need to prep the ship again.