This is a violation of every customer's rights. This is not a case of some locations not participating, since the company goes as far as to call the product the "$5 BOX." That means it costs five dollars, and if it doesn't, it can't be called that. I hope you obtained some compensation from corporate for your hardship.
Most often when a fast food customer pays a number that doesn't sound right it is because a single worker, group of workers or even the manager is supplementing their low wages by fabricating charges and pocketing the difference. Everyone knows fast food workers are largely ex-cons that know how to run a scam, and teenagers naive enough to join in. On those grounds, make sure corporate knows what you were charged for what items.