I have also been a victim of an unexplained higher charge than what was expected, but it had nothing to do with extra mileage, damage, or anything else for that matter. I have only ever rented a car twice in my life.
Brief history: Became Velocity Gold status, linked up with a major car rental company, automatically got elevated a couple of status levels with them, planned a holiday months in advance, selected a car, was given a free upgrade when we picked it up, received an invoice receipt a few days after getting back home for the same amount as the original quote.
Second time, still at the same status level I planned another holiday well in advance, selected a car, was given a free upgrade when we picked it up, received an invoice receipt a few days after getting back home for a higher amount than what was quoted, by about 10%. No explanation. I sent an email via their website and was refunded the difference a couple of weeks later, but again, with no explanation.
I'm still confused why I was charged more. Even by the invoice I was under the km allowance and I returned the car full of fuel, there was no (additional) damage, and it was returned on time. I assumed it was because of the "free" upgrade, but I had already had a precedent set in place, and the car had the same category code as what I had originally chosen. Those factors formed the basis of my argument in the email.
Although I was successful in being refunded the difference, it sucks that the onus is on the customer to chase it up.