So, I just went to Walgreen's to try this out. Rang up items, held phone to pin pad, used my fingerprint, transaction was accepted. Then, the pin pad asks for my PIN number. I thought ok, I was using my B of A debit card. Entered the PIN, transaction went as normal. I get home, check my B of A app, and there are TWO transactions pending from Walgreens. Same amount. I call B of A and none of their customer service representatives even know what Apple Pay is. I have to wait until the transactions post before they will initiate a reversal. I called B of A twice, the second time hoping to get someone who knew what was going on. The second representative said that it's showing I entered my PIN twice, about 20 seconds apart. I said no, I only entered my PIN once. I had to explain to both representatives how I paid (each time they said "how many times did you swipe the card?" when I said "I never swiped the card" you could almost hear their heads exploding).
I'm guessing that I should have never entered my PIN number when asked. I should have just hit credit. If you have used Apple Pay anywhere and entered a PIN number, I would suggest checking your bank statement.