I have a sneaking suspicion that she originally bought an "S" trim model and when she was getting in and out, she was scraping the side panels unique to that trim. They put her into a base (VERY base, with roll up windows) model, gave her butkus for her trade, and then added on every warranty/fee/etching/crap they could find.
I also am willing to bet that they made it sound like they were taking her existing car back and "giving" her a new one. "Oh, we'll put you in this model that won't have that pesky paint problem." But of course your existing car is used, so you might have to take a few less options on your new car.
The dealer got a spanky trade for low money, got a base model off the lot, and made a ton of dough.