Does the milage on the rental paperwork match what they said on return?
I had a rental recently from a HLE to LAX. Mileage on the rental paperwork was correct at time of rental, but on return the paperwork claimed I'd done about 500 miles (impressive given that I had the car for about 5-6 hours). When I checked, the starting mileage on the return paperwork didn't match the starting mileage on the contract.
It was an unlimited mileage rental so I didn't bother doing anything about it, but it's something else to check if you're on a per-mile rate.