Issue checking out at the supermarket

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I decided to buy hummus yesterday. The supermarket had it on sale. Buy one for $3.99 get another one free. I was gonna buy two anyway so that was a good deal. When I scanned both, in the self-checkout register, $3.99 was not taken off, so I called for help. When the lady came over and I told her what happened she told me to proceed with the checkout. I had to click that I am ready to pay, select how many bags I used (they now charge 5 cents per bag), and if I have any coupons. After I did that it took off the $3.99. The lady told me that next time I should first do this step and if that doesn't take off the discount only then should I call for help. That sounded rather rude to me but at least now I know to do that. But this whole thing makes no sense to me. Why was the system designed to do that? If there are any discounts that should be applied (not counting coupons) that should be taken off right after I scan the item and not after I do all the other steps...