Can't be just an oversight. This has to be an intentional design decision. The "simple" (and economical) way to build this system is to build it so that the scan reads the price from a database and that price is then displayed and used to sum the total.
Keeping two prices, a display and a real one, is a design decision that adds a complexity to the system, makes it more difficult to administer and is an intentional design decision, especially if the numbers are allowed to differ.
A coupon not being applied correctly could be a mistake with that coupon. A sale not being taken into account, a problem with that sale or that UPC entry in the database. Those could be issues with data entry and data management.
This is different. This is intentional. And I'd bet, we've just found someone either cheating the tax man or embezzling funds.