my opinion is
you only pay based on what you got
you should inform the makers of the 1099 to remake the 1099 based on the true funds or show the canceled check.
If you cashed the check and then handed it back a whole other story.
then you might ask you tax person to expense it.
Harold Sharpe - Broker
So Cal Homes Realty
California Department of Real Estate Broker License # 01312992
Building on Lance's comment: submit the closing statement as evidence and request a corrected 1099 from the Broker's office. You never received the $500 so I'm not sure it would qualify as a deducible expense.