I'm sure that every company handles it differently. However, I did witness this years ago from the retail end.... The cashier in question was written-up and retrained. He was then sent back to work with the knowledge that a second offense would lead to his termination. On the flip side, a cashier caught by an ATF sting was immediately terminated and faced legal charges. If a certain business fails too many ATF stings, it is heavily fined and loses its license to sell said products.
I see this compliance audits as a favor to the failing cashier and business. It's much better to be caught by a shopper than the authorities.
Hard work builds character and homework is good for your soul.