Mobile payments are booming. But are you missing out on credit card cash-back bonuses and rewards if you use your digital wallet?

You could be. On its rewards information website, American Express warns that cardholders may not receive rewards points in eligible categories if they use digital wallets like PayPal and Google Wallet. Other card issuers, such as Chase and Discover, sent out notifications to cardholders this spring that purchases made through mobile apps may not qualify for reward points if the technology is not set up to process the purchase in that reward category.

In other words, if the mobile app purchases are incorrectly coded, issuers may not be able to identify them as qualifying for a rewards.

That's exactly what's happened to some digital-wallet users, mobile payments experts say. "This has primarily been an issue with Google Wallet and other digital wallets such as PayPal," said Kari Luckett, content director for credit-card ratings website CompareCards, who looked into the issue after receiving some complaints for digital wallet users. "The problem is that they have a card on their back-end that most consumers aren't aware of."

Although the customers have added their rewards cards to the payment app, she said, "the card being used to pay for the transaction is actually the card Google has behind-the-scenes. Then that card is later reimbursed with the real credit card."

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When someone uses the PayPal digital wallet at a merchant with a credit card in a category that offers rewards, such as a gas station, the transaction shows up as a PayPal transaction with the card issuer, not the merchant code of the gas station. "It's always been a challenge for PayPal," said Cherian Abraham, mobile commerce and payments practice lead at Experian's Global Consulting Practice. "When the merchant is masked, users are not able to receive category-driven rewards."

Apple Pay, the digital wallet on the iPhone 6, avoids this problem by working directly with the banks, Luckett said.