The rapper blamed technical difficulties for the pre-recorded track played over the ceremony's TV broadcast.
"U could hear me in the auditorium but apparently not in TV land," she wrote on her Twitter page. "Shout out to the sound guy."
She added: "They say it'll b fixed wen it re-airs (sic)."
Minaj won the awards for Best Female Hip-Hop Artist and Best New Artist, as well as a trophy for Best Group with Young Money.