This is fairly common practice at most fast food chains. They are trained to "suggestive sell" to try to move as much product as possible. It may be from habit to ask, and I agree it IS frustrating when mistakes happen after repeating the order.
I don't think writing to corporate after the fact for reimbursement for a meal one actually ate is as effective as bringing the receipt and the product up to the cashier. The whopper with cheese is a seperate line item, and if I recall correctly, it's a bit more expensive.