What card was used as the payment method? You have the option of filing a dispute with the bank that issued the credit or debit used, or request a refund with the merchant. Merchants generally don’t want a dispute, it costs them additional time and expenses to defend against a dispute. You shouldn’t do both at the same time, but once you’ve exhausted the refund request process, go ahead and dispute the transaction. Doing both at the same time can sometimes lead to fraud situations if both the refund and dispute are approved.
Apple Pay is just the pipeline or system through which the data for the original transaction was conducted. The refund if approved will go directly from the merchants bank to your credit card bank as a credit. If you go the dispute route the amount of the transaction will immediately be credited to your account. If you lose the dispute the credit to your account will be reversed.