Yes. I got double charged at Walgreens. I'm on hold right now with Bank of America because, both charges posted to my account. Yesterday, when I called, I spoke with 2 different customer service representatives, both of which had no idea what Apple Pay was. They both asked me "how many times did you swipe your card."
The Walgreens pin pad terminal asked me to enter my PIN after I used Touch ID to verify the purchase. I entered it, because it was my first time using Apple Pay and figured, "well, since its a debit....." so I don't know if that was what messed it up or not.
B of A is "disputing the charge" as a "posting error," and the gentleman I spoke with today said I was the second person he's talked to that got a double posting like this using Apple Pay. However, he did ask me how many times I swiped my card.