I haven't had this happen with National, but it happened to me all the time at Hertz. I would return it full and refuse to stand around in 100 degree heat at DFW waiting for someone to make their way down the massive line of cars. They would check it in and charge for a full tank (not even looking at the guage?)
Each time was just a phone call to the corporate number and the charge was removed. I would assume national would be the same.