It costs a culture token and a ship in that sector...do you "pay" the ship by removing one? Or do you just have to have a ship present in order to pay the culture to establish a control node?
You need a ship in the system to attempt Hegemony (no rival ships - ally or enemy - can be present). One Command token is exhausted and one culture is paid to attempt Hegemony. If successful you pay another culture and remove a ship in the system to put your Control Node on the planet. If you fail, you can exhaust another available Command and spend one culture token to try again.