You are likely being charged extra for repairs because you do not have sufficient resources to repair your fleet. It is a common misconception that, when you coin a fleet repair, you do not pay the resource cost. This is not, and has never been, the case. When you don’t have sufficient resources to repair a fleet, the game includes the price of purchasing all necessary resources into the final “Instant Repair” cost.
With full warehouses, the damaged fleet below only costs 35 gold to repair:
However, when there are not enough resources to cover those repairs (note that the resource totals for Metal, Energy, and Zynthium are all red) the cost to instantly repair the fleet becomes much higher: