The complaint must be filed with the rental office where the car was picked up. Even if the reservation had been made through the website of a domestic car rental company, the actual rental agreement is usually concluded only when the car is picked up, with the rental company there.
These types of fees are usually the repair cost of a car that the rental company considers to have been incurred because of damage caused by the renter. It may also be administrative costs incurred by the car company as a result of fines to the consumer. It is therefore a good idea to check the credit card balance regularly after the rental period. You will find instructions on avoiding billing afterwards here.