The news network on Tuesday acknowledged that a producer went "too far" in telling Brown University student Alexandra Trustman what to ask.
CNN televised the debate, co-sponsored by the nonprofit Rock the Vote organization, last week. It was billed as an event geared to the interests of young people.
CNN spokeswoman Christa Robinson said the cable network regrets the producer's actions. She would not identify the employee.
"In an attempt to encourage a lighthearted moment in this debate, a CNN producer working with Ms. Trustman clearly went too far," she said. All of the other questions from the audience originated from the person asking them, she said.
In an editorial written for the Brown Daily Herald, Trustman said she was called the morning of the debate and given the topic of the question CNN producers wanted her to ask.
Trustman said she was "confused by the question's relevance," and constructed her own question "about how, if elected, the candidates would use technology in their administrations."
But when she arrived in Boston for the debate, Trustman wrote, "I was handed a note card with the Macs and PCs version of Clinton's boxers or briefs question" and told she couldn't ask her question "because it wasn't lighthearted enough and they wanted to modulate the event with various types of questions."
She referred to a 1992 student forum where Bill Clinton was asked what kind of underwear he preferred.
A message left Tuesday for Trustman was not immediately returned and she did not respond to an e-mail from The Associated Press. A woman who answered Trustman's phone said Trustman did not want to comment.