The song that had been used was "Milkshake" by the artist Kelis, who was upset when she heard about the use of her work.
This is reported by Billboard, among others.
Kelis sang on the song "Milkshake" written by The Neptunes - Pharrell Williams and Chad Hugo - but only the producer duo are credited as songwriters.
Kelis claims she was duped into signing a contract that means she is now not making any money from the song at all.
Kelis posted an attention-grabbing post on Instagram explaining how disappointed she was that Beyoncé didn't hear back, saying that "the level of disrespect and total ignorance on all three parties is astounding."
Monica Lewinsky also critical
Now the "Milkshake" part will be removed from the song "Energy" on Apple and Tidal.
This comes just days after Beyoncé changed another of the newly released album's songs, following accusations of funkophobia in a lyric.
After it became clear that that line of text had been removed, Monica Lewinsky also suggested in a post on Twitter that Beyoncé should remove a line of text with her name from the song "Partition" from 2013.