Apple Pay, the mobile payment system available in the newest versions of the iPhone, has hit a snag. When Tim Cook announced the new mobile wallet during Apple's fall product event, he made it clear that Pay was launching with full force, with a long list of retailers already on board. Six banks signed up, along with Bloomingdales, Panera, Sephora, Groupon, Subway, Disney, Target, McDonald's, Whole Foods, Macy's, and Walgreens. Two big retailers, however, are taking a stand against the mobile payment system: Rite Aid and CVS.

Although the technology—which allows you to pay at checkout counters by swiping your phone, rather than a credit card—worked when Apple Pay first launched early last week, over the weekend, both companies disabled Apple Pay in their stores.

It's not just a shot at Apple, however. Google Wallet and Softcard, similar e-pay products, were also disabled. Ashley Flower, spokesperson for Rite Aid, told CNBC, "[Rite Aid] does not currently accept Apple Pay. [We are] still in the process of evaluating our mobile payment options." CVS has not commented, nor has Apple. Flower told Business Week, "We are continually evaluating various forms of mobile payment technologies, and are committed to offering convenient, reliable, and secure payment methods that meet the needs of our customers."

There is speculation that this decision was made in order to make way for CurrentC, a rival product spearheaded by Walmart that is set to hit the market in 2015. About fifty major retailers are said to be involved with CurrentC, which offers a major incentive for the brands: CurrentC does not collaborate with credit card companies, it eliminates them all together. This, in turn, cuts down on card transaction fees and helps the bottom line for retailers. It is unclear when exactly CurrentC will launch, nor how the product will work on the consumer end.

As for card providers, they believe Rite Aid and CVS should reconsider. Ed McLaughlin, MasterCard's chief emerging payments officer, told CNBC, "We think consumers should have the ability to pay any way they want. Rite Aid and CVS have been accepting contactless payments for quite a long time. We look forward to them turning the functionality back on in their stores."