Store coupon frauding

So we are always hearing about "couponers" committing coupon fraud but what about the stores themselves? I have had a few problems lately with stores modifying the coupon and not applying the overage to the remaining items in my basket. I asked an employee about this and she explained that the stores (in this case Krogers) turn in the coupon to the manufacturer at face value. That is fraud either way you look at it. What can we as couponers do about this?? It is not okay for any retailers to take a coupon at face value and turn it in at face value but only allow the customer a "modified" amount. Free or not...its wrong.