If they don't have the vehicle you booked then they should provide you with something else-- at no extra charge. They should not charge you an upgrade fee unless you specifically asked for something else. If they try that complain. If they still give you a hard time, tell them you want the contacting information for the district manager and start escalating.

Just be sure that you're authorized to use any corporate discount code that you apply. You don't want them to have an excuse to deny you the rate you originally booked.