The "X" flashed twice, on the air for a total of one-seventh of a second, CNN said Wednesday.
The incident caused a brief sensation on the Web among people suspicious that it was a political commentary. But CNN said some of its machinery had a "momentary glitch" and no human operator was involved.
The "X" is something used by a computer to mark a space where one visual element is to segue into another, and is normally not seen by a viewer. The network likened its appearance to a computer that inexplicably freezes.
"We obviously regret that it happened and are working on the equipment to ensure it is not repeated," the network said in a statement.