You simply failed to realize what Apple Pay is. The sole purpose is to securely proved the merchant a unique token provided by your bank when you added their card. That way the merchant does not have your actual account number to the credit card you used to prevent your account number from being sold on the dark web in case of a data breach or from a bad actor. That does not change the way you dispute any credit card purchase. The first thing you do is contact the merchant and if not resolved, then you dispute the charge with your credit card being billed. Any refund provided by the merchant goes directly to your credit card, it does not go through Apple Pay as Apple is not involved at all.
The alternative to using Apple Pay is to give the merchant your actual credit card number. That is the reason why you should be using Apple Pay, so the merchant does NOT have your credit card number.