Unfortunately, this sort of thing is not uncommon outside the U.S. Like most non-US/CA locations, Thrifty in Uruguay is a franchised location owned by a local operator. Hertz (who owns Thrifty) doesn't really have the power to force them to do anything, but I believe there is some sort of chargeback process that can be initiated by Hertz corporate in the case where a customer has been incorrectly charged. Something it can be arduous to get them to admit wrongdoing though.

I would recommend filing a grievance with Thrifty corporate using this web form. Be specific and to the point about what you experienced and be clear and reasonable about what you expect Thrifty to do to resolve the situation (like honor the original rate and credit you for the upgrade charge). You can mention that you want to give them the opportunity to make things right before you are forced to escalate the matter and file a grievance request with your credit card company (which they would typically like to avoid).

If that doesn't work, reply back and we can advise on next steps.