A Bank of America spokeswoman said the issue affected about 1,000 translations, but she declined to offer details about the suspected cause of the glitch.
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"We apologize for this inconvenience and are correcting this issue immediately. All duplicates will be refunded," spokeswoman Tara Burke said.
Apple told CNBC that it was aware of "a Bank of America issue impacting a very small number of Apple Pay users."
Bank of America and Walgreens responded to the tweet and the user later said the claim was resolved.
MasterCard, which handles the Bank of America's Apple Pay transactions, said it was unaware of any issues involving its processing system or Apple Pay customers.
"We're the network behind it but the issuers are the ones that holds that customer relationship," the company said.
MasterCard has signed deals with "hundreds of issuers" who plan to offer Apple Pay via its networking equipment.
Apple Pay, which launched earlier this week, lets iPhone 6 users make in-store purchases using tap-to-pay wireless terminals.
The company has touted the new platform as a "secure and private way" to make purchases and said more than 500 banks and 22,000 retailers plan to support the feature by the end of the year.
"Apple doesn't collect your purchase history, so we don't know what you bought, where you bought it or how much you paid for it," the tech behemoth said in a statement Monday.