I had exactly this in Vegas last summer, except it was obvious when they handed me the bill at the end rather than when I got home. It took the location manager (who, to his credit, really cared about fixing it there and then) the best part of an hour to fix. He had to log into a separate, apparently obsolete computer system that is needed sometimes to fix really intractable problems.
He he said it would be possible to leave and get it fixed later, but obviously felt that a better customer experience would be for him to fix it at the time.
I think mine arose arose because I picked the car up at about 4am the next morning rather than late at night when my flight had arrived. I had cleared this with both Avis and ba hols in advance.