Scattered reports of double payments and failed transactions have begun to bubble to the surface after what initially looked like a relatively smooth introduction of Apple Pay.

Some Bank of America customers reported Tuesday that they were charged twice for purchases made through Apple's new payment system. One was a CNN Money reporter who described his experiences being double charged and the difficulties he had in getting the issue resolved.

Bank of America acknowledged the problem, but said it was limited.

"We apologize for the inconvenience and we're correcting the issue. All duplicates will be refunded," said Tara Burke, a spokesperson for the bank. She said that roughly 1,000 of the bank's customers had been affected.

The issue was likely a coding problem on Bank of America's end, according to Cornerstone, a Scottsdale, Ariz.-based consulting firm. Burke declined to comment.

Some of Cornerstone's clients who were part of the first wave of financial institutions adopting Apple Pay experienced a different problem on Monday, the day the program debuted. They reported feedback from customers saying their phones rejected the Apple Pay transaction because their institution wasn’t supported.

"There are more problems than just this Bank of America issue," said Bob Roth, Cornerstone's payment practices manager. Roth said that Cornerstone had not canvassed its clients but he did not believe issues were widespread.

"New technology's always going to have issues three days in," Roth said, adding that he thought Apple Pay's overall debut had been "pretty impressive."  A representative for Apple did not return a call by deadline.

Two of the vendors transitioning merchants and financial institutions onto Apple Pay agreed. 

Pete Donat, head of new ventures for payment security and infrastructure provider First Data, said Tuesday that the company’s clients, including several of the first banks to adopt Apple's new one-touch payment system, had seen few problems with the mobile payment rollout.

Like First Data, Chase's mobile payment division also helps clients with the infrastructure necessary to use Apple Pay. Chase mobile's general manager, Tom O'Brien, said that though the company "found a lot of things that we fixed along the way" to Apple Pay's debut, so far it's provided a, "really smooth, really secure customer experience." According to O'Brien, Apple Pay signups by customers on Tuesday were seven times higher than traditional card enrollment—a one day snapshot but an indication of momentum and adoption of a new product on the consumer side. 

That momentum seems to extend to the financial side as well. "The banks we're talking to are generally excited about the opportunity to participate in Apple Pay," Donat said, saying that he predicts thousands will soon follow the more than 500 that have already agreed to support Apple Pay.

Roth, of Cornerstone, said the big question surrounding Apple Pay will be how the experience goes for that first wave of adopters.

Chase and First Data both provide physical platforms that support near-field communication transactions, which mobile payment systems like Apple Pay and Google Wallet use, but both are also among the that provide application program interfaces (APIs), allowing developers to integrate Apple Pay as a payment option for their applications.

"We think in-app payments are going to be one of the higher growth areas," Donat said. "Apple's done a good job, as have the networks and others involved, of riding on an existing standard," of protocols for tokenization.

One early complication that customers have seen is double payment.  Tokenization, part of Apple Pay's security, made troubleshooting the issue problematic: in the Apple Pay transaction personal customer information is not transmitted, which makes it hard for Apple to track the double payment issue until customers began calling. 

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