It looks like they did explain,though. Besides the ad (which states there's an extra charge for the stuffed crust) the employees told you at least three times. So you decide to complain to the company about it, and the store owner has to explain yet again. Even when he highlights where it states "Extra charge...", you feel the need to go to corporate again. Maybe you should be the one writing the nice apology letter for the misunderstanding, as you've now been told about a half dozen times.
BTW, there's an extra charge for stuffed crust.