Why is it the customer's responsibility to figure out and comply with the rules of your (nonstandard) system to avoid getting charged for something they don't intend to buy and didn't in fact use or take out of the store?
There are all kinds of reasons why that is unreasonable:
* different stores might have systems with different rules and policies, causing confusion;
* people may not remember where to return the item;
* the magic machine-learning system might glitch and not recognize the item was replaced, and you probably won't notice since there's little feedback from the "virtual cart" since you're not interacting with it directly;
* another glitch could put another customer's item in your "virtual cart", so you have nothing to return;
* etc.
Systems like this should fail in customer-friendly ways, and "item returned to the wrong place" is a kind of failure.