This still does not answer the question. In what specific ways was the cost higher?

It goes without saying that the voucher is applied as a credit. But, if all is well, the voucher should bring the balance to $0. So, the question remains, what aspect of the invoice was different?

SFO, by way of example, has specific concession taxes which are entirely separate from any other tax or fee charged. Those are collected by Hertz, but yours to pay. That is just one example.

It would be helpful if you would compare the two invoices showing how the prepaid was calculated and how Hertz later calculated to come to a different number. Without that, it is of little use to others.