Yes, had an instance of this in Japan recently. They charged over the internet confirmed rate. Not much over but I am still negotiating. The American internet booking agency (starting with "E") did not want to know anything about it.
My strategy next time will be to have the rate confirmed and signed off when I book in at the front desk.
Can I also suggest if you are ever travelling on a code share flight that you check with both airlines as you may be surprised to find the fares are not always the same.
Sad isn't it when dealing with large companies who feel it is fair game to try to rip you off.