Was it a 1-way rental by any chance? Those usually come with per-mile charges, regardless of which corporate code you use.
If there's a per-mile charge it's usually listed in the rental agreement that you got online and they printed for you when you picked up the car. If its unlimited mileage that's usually specified as well.
If the contract specified a per-mile charge and you just overlooked it, that's nobody's fault but your own.