Apple Pay has been charging some Bank of America customers twice since the launch of Apple's mobile NFC payments system at the start of the week.
Roughly 1,000 transactions made with Apple Pay were logged twice in customer accounts, said Tara Burke, a spokeswoman with Bank of America, which is one of the largest US banks and was an Apple Pay launch partner.
"We apologise for the inconvenience and are correcting the problem," said Burke.
Apple Pay utilises a secure chip inside Apple's new iPhone 6 that enables the phone to emulate an NFC (near field communications) payment card. When the Apple Pay app is loaded with a customer's credit or debit card, payments can be made at NFC terminals by bringing the phone close to the terminal.
The system is being positioned as easier and more secure than current payment cards because the card number is not passed to the retailer's terminal. Instead, a substitute number called a token is offered to the merchant, which sends it on to the card issuer for approval.
The token can only be used once, so if it's stolen it should prove useless to cyberattackers. It's tied to the actual card number deeper in the financial services network, further away from the retailer terminals that have been the target of so much hacking recently.
Apple Pay is compatible with existing NFC payment terminals, which can be found in around 200,000 shops and taxis across the US.