A pop-up could more easily do that without being annoying. "You already scanned Miracle Food. How many total are you buying? Just one / enter a number / I'll scan each one manually"

More likely it's for absent-minded customers who don't realize the item didn't scan. If there's a sudden weight without a new barcode scanned, the error message on the machines at the store I use say something like "unexpected weight, please remove item and scan again".

In the early days of self checkout I remember being behind a woman who could not figure out how to scan things. She was basically presenting the items to the scanner like it was a photo shoot while getting frustrated that the machine only sometimes recognized what she was presenting to it.