During the live performance of Beyoncé and Sean Paul's "Baby Boy" (near to Paul's rap), the backing tracks of vocals ("Baby boy you are so damn fine") started to malfunction, failing to repeat and losing the instrumental part of the song. Through the technical difficulties, Paul sang for a bit; Beyoncé asked the crowd how they were doing, which received applause and cheers.
The malfunction of the backing track vocals was cut from the live airing on TV but still played through the venue. Both artist and the dancers exited the stage, which then resulted in confusion among the presenters. When Christina Aguilera walked onto the stage to continue the event, the musical track stopped playing again. After Pink presented the award for Best Album, the duo was asked if they would like to do a re-take. Both agreed and performed the song as rehearsed. The re-take would replace the original take on re-airings of the show. This caused the EMAs to be extended, which had never happened before.