Some Realtors will charge an additional fee simply for processing a Short Sale or if they use a service company to do the processing of the short sale transaction. However, these should have been disclosed to you up front if they would apply in your situation. I do not charge additional fees other than the standard commission that I would earn on a real estate transaction when it closes.
In addition, you may find that there may be some costs that you may need to pay for that are part of the negotiation process in order to get the sale closed as the Seller's Lender will want to net a particular amount. Also, sometimes if all costs were not on the initial preliminary settlement statement and they appear on the final settlement statement it would be difficult to get the Seller's Lender to go back and adjust their net amount as they do not want to receive any less. Therefore, when this situation would occur, these extra costs need to be paid by someone and typically the Seller doesn't have the money and will be looking for the Buyer to pay for the costs. This is okay, if there's room, if the Buyer is receiving a fabulous deal. Basically, these additional costs can be eliminated if the Realtors involved in the transaction are in the know when it comes to short sales. Hopefully, all your costs have been accounted for. Best wishes to you.