The heart is the seat of emotion. When Vanitas forces his emotions outside of him to create the Unversed, it's akin to a piece of his heart going along for the ride. It is a painful experience, but so is taking back in that part of himself. And Vanitas? He hates that. Hates all of it. Hates that he can create them. Hates that it does hurt.

To hear Sora say he's not attacking them... "Why? I do."