In Arizona, there are registration fees that go to the state, but the dealers also add in what looks like an official charge, "Dealer Documentary Fee," which I explain to my clients means "Additional Dealer Profit."  Just one of the many ways they transfer money from the buyers' pockets to their own.  Often it's printed on the contract, so it can't be negotiated (you just have to realize it's in addition to the price of the vehicle).  

I have seen this in another states also, I think some of the more consumer-friendly jurisdictions put a limit on how much it can be.  45 years ago it was usually only around $30, and was a fair price for the clerical work involved in doing the paperwork. One used-car dealer told me that for many sales, the only real profit was in the "dealer documentary fee."  

To answer your question -- if you expect an IRS audit to match bank deposits with tax return gross income, just subtract it the actual fees as part of cost of goods sold.