Some industry analysts, such as Gartner Inc.'s Joe Unsworth and IDC's Celeste Crystal, aren't as concerned about USB flash drive fragmentation. Asked if he believes if defragging flash memory is a good idea, Unsworth said simply, "I've not heard of it."

"It's not something that has become a very big issue with the USB flash drive market," Crystal added.

But a problem that is becoming bigger for this technology is manufacturing quality control, according to a recent report by the Australian firm Payam Data Recovery Pty. (PDR). Cases of faulty USB flash drives are on the rise the point where there has been a 300 percent year-over-year increase in cases of USB drives that have "suddenly stopped working" as a result of "faults, misuse and an increasing number of poorly manufactured devices on the market," according to PDR's study.

"I would expect that you would see an increase in problems with USB flash drives because they're much more pervasive and there are a lot of companies that are [manufacturing] them these days," Unsworth said. Many of the companies producing flash memory are based in Taiwan, Singapore and China, and Unsworth said that Asia-Pacific distributors are trying to differentiate themselves on price, which is forcing many market players to follow suit. As a result of this price pressure, some companies are selling products based on inferior flash memory, he said.

Steffen Hellmold, president of The USB Flash Drive Alliance, said he doesn't believe that fragmentation presents a problem with flash memory, but he does agree that quality control has been an ongoing issue. "There are issues around endurance and longevity," he said.