Holiday gift cards the latest problem for Target

Some shoppers who received a Target gift card this holiday season may find that redeeming it requires some work.

Target confirmed Tuesday that a number of gift cards sold during the holiday period were not fully activated, so shoppers attempting to use them would find they had no value.

A display advertising Target gift cards at a store in Mayfield Heights, Ohio.
Amy Sancetta | AP

The snafu comes at a tough time for Target, to say the least. The company recently announced that a data breach in late December had affected an estimated 40 million debit and credit card accounts used to make a purchase at a Target store during the holiday rush.

This incident is unrelated.

(Read more: Why did Target take so long to report the breach?)

Widespread gift card bugs and activation errors are unusual, according to Dan Horne, a professor of marketing at Providence College.

"This is really rare," he said. "Generally, the accuracy of gift cards is phenomenal. The reason they have taken off is that they work."

A Fox station in Minneapolis reported that the foul-up could affect as many as 40,000 cards—a figure Target disputed.

"The numbers that have been reported in the media are much higher than what we experienced," Target spokeswoman Molly Snyder said in a statement. "The actual number of cards impacted was less than 0.1 percent of the total sold during the holiday period."

Still, that could be a substantial number of cards and balances in limbo.

Gift card purchases this holiday season were expected to total $29.8 billion, according to the National Retail Federation. Department stores, including Target, were the top gift card category, with 40 percent of shoppers saying they planned to buy at least one card from such a retailer. The average card value was $45.16.

(Read more: The most requested gift cards)

Can Target win back customers?

Target will honor affected cards, Snyder said.

"If a guest discovers that their gift card has not been activated, they can bring it to the guest service desk at their local Target store or call 1-800-544-2943 for assistance," she said.

The company did not respond to requests for comment on how it would determine the balance that should be loaded onto the card.

Most retailers' systems can track gift cards by looking into records for the card, including the point of sale, according to Horne.

"If they have the card number, they should be able to track it," he said.

The incident reinforces an important point for shoppers, whether they are buying a gift card, getting one for free with a purchase or receiving one for store credit after a return.

"Whenever you get a gift card, make sure you keep the receipt in case it didn't take," said Edgar Dworsky, founder of "If you really want to be thorough, call the toll-free number on the back of the card and check its balance."

—By CNBC's Kelli B. Grant. Follow her on Twitter @Kelligrant and on Google.