The singer was stunned when a man dressed partially as a woman took the stage to perform her song '(You Drive Me) Crazy', according to People.
Spears eventually returned and insisted that she was not offended by the man's performance.
"I really respect the tribute," she said. "It was really nice."
Fellow judges Demi Lovato and LA Reid followed Spears off the set, while Simon Cowell stayed behind.
"I don't think she quite understood your tribute," Cowell told the singer.
Meanwhile, the man was driven to tears, telling the judges that he almost missed his X Factor call because he could not afford to pay his phone bill.
"I had to fight real hard to get here," he said.
During the same day, Spears was filmed dancing while a contestant rapped a version of Vanilla Ice's 'Ice Ice Baby'.
The X Factor USA premieres September 12 on Fox.
Watch Britney Spears show off her dance moves to 'Ice Ice Baby' below: