It depends. Are you new to cashiering by chance? I haven't had much issue with that myself, although, as someone who was in Recovery in the Food department for almost a year, I was already used to making a lot of similar motions while working, so it didn't bother me to switch to Cashiering, and I go pretty quickly while scanning and bagging.
If you're not new, it's likely an issue with your technique or the positioning of the counter and bags that you're working with. Do you have any more information about the layout of your area? The height of the scanner for instance, location of bags, how you're scanning? All these things can affect the way your shoulders/back feel after a day of work.