The early glitch saw Bank of America customers getting charged twice for some purchases – although the fault appears to lie with the bank rather than Apple.
A Bank of America spokeswoman confirmed the issue to the US press and said around 1,000 transactions had been affected.
"All duplicates will be refunded, we apologise for the inconvenience and are correcting this immediately," the spokeswoman told CNET.
Apple Pay is off to an amazing start and customers are loving the easy, secure and private way to pay
An Apple spokesperson placed the blame squarely on Bank of America's shoulders, and said most users weren't experiencing any trouble.
The spokesperson said: "Apple Pay is off to an amazing start and customers are loving the easy, secure and private way to pay,"
Apple Pay was announced in September, alongside the new iPhone 6 and larger iPhone 6 Plus. The payment service enables users to register their card, then simply tap their devices on compatible terminals to pay for items.
The app works using near-field communication (NFC) technology, and is only available on the iPhone 6 and the iPhone 6 Plus.
The service also allows users to pay for items through other supported apps, which has proven a bumpy process. There are fewer than 20 third-party apps compatible with Apple Pay, and these exclude major players such as Amazon and eBay. And, according to the New York Times, compatible apps are not particularly easy to use.
For example, a user trying to pay for an Uber cab has to go through multiple steps to authorise a payment. Likewise for paying for items bought from US store Target.
"There is a lot to like about Apple Pay, but this ship has holes," notes Forrester analyst Denée Carrington. "And if not addressed, these 'misses' will derail Apple Pay's ability to go mainstream."