Of the many features that come with the iPhone 6 and 6 Plus, Apple Pay has some noticeable issues already. It's a grand idea that Apple Pay will let users tap the device to a terminal instead of pulling out cash or a credit card to pay in a store. One issue that consumers should be aware of is that not too many stores actually have Apple Pay yet.

Stores need to first upgrade cash registers to the Apple technology.

Currently, 220,000 retail locations will allow these purchases, but that's only 5.5 percent of all retail outlets in the United States.

As far as security goes, Apple says consumers and retailers are safer using Apple Pay than a credit card.

The Touch ID is a fingerprint identification system. Apple says it will make the transaction safer for two reasons: the uniqueness of your fingerprint and because the cashier will never see your credit card.

In addition, Apple Pay uses EMV (chip and pin) technology, a security system already used in Europe on plastic credit cards. "It's a lot safer than the information that's stored on the magnetic strips on the back of our credit cards that we use here in the United States," said John Simons, technology and media editor at The Associated Press.

—By CNBC's Christina Medici Scolaro