Just get into the habit of washing your reusable bags after unloading groceries at home. Yes they can house viruses and bacteria, same as everything else in the world, but if you get cloth bags it's super easy to toss them in the laundry machine and if you get plastic ones there exists sanitizing wipes and spray. And if you're using the Wegmans Scan app or self-checkout you'll be the only person who touches your bag which should limit the spread of pathogens too.
If you really, absolutely, hate reusable bags you can purchase disposable plastic bags online (350 for $16.99 on Amazon) and bring those with you to the store. Only difference is they won't have the Wegmans logo on them.
The paper bags are really only there for people who didn't bring their bags or bring enough bags, and the charge-per-bag is incentive for people to start bringing their own. Those paper bags aren't much healthier for the environment than the disposable plastic bags.
If the Scan app is that broken (I would not be surprised), use something like Tasker to silence media volume while the app is open and restore it when it isn't.
https://play.google.com/store/apps/details?id=net.dinglisch.android.taskerm