Although I have had the same issue using both Walmart and Kroger $5 e-gift cards. And, yes, I was watching how it was applied to my bill. The first time I used it at Walmart they said something about it trying to load money on the e-gift card rather than applying the balance of the e-gift card to my bill. After realizing that the register may want to add funds to the card, then it has been easy to explain to an experienced cashier or to a front-line manager that comes to help when it happens.
Frankly, I try to watch as items are scanned, whenever possible, because grocery store price errors have become commonplace. (Remember when: the price was on the product and the grocery "checker" had to enter the price on the register and paper coupons could be 5ยข off.)
AndrewToo