Not all store registers are the same, some have the option for Credit or Debit and the cashier typically will ask you beforehand and they press the credit option on their end allowing your to use Apple Pay/Google Wallet.
The problem is places like Home Depot (i used to be a cashier there) have a single button on the cashiers screen for Debit/Credit, we press it and the customer has to swipe the card, enter pin or cancel to run it as credit.
The register needs an update to make it two different buttons or to recognize when NFC payment is being taken.
If you are using Apple Pay with a credit card then the problem goes away, it only affects the debit card with visa/mastercard logo. This is why Apple Pay is working in many places that are not advertised by Apple.