This could be fear-mongering by the anti-music groups, or it could be a stunt to give Skepta more attention/credibility. Or it could literally be false or an otherwise non-story.
Of course, it can be true after all. It just sets off alarms in my head saying "this doesn't seem vetted."
We may not know why the complaint was issued, but we know that the artist released it on his own YouTube account and we know that the video was replaced by a copyright notice. Those are all things that any person browsing the web could verify for themselves.
Only the copyright holder or their agent can authorize a DMCA notice, so it's pretty hard to understand why the artists own upload got taken down.
There were tons of stories about companies (especially TV studios, I believe) where the PR/Marketing team would post stuff to YouTube, and then Legal would file DMCAs to take it down. I believe that was even a part of the lawsuit against YouTube. So, the idea that something similar happened here isn't ridiculous, especially if Skepta thought he had rights to the music he signed away that he did not in fact have.