Yuya just failed NTR 101. He hasn't seen enough hentai or JAV in his previous life.
He's relying too much on the "brainwashing skill" but doesn't have the capability to back it up. His current process is setting him up for betrayal. He couldn't make them believe they like it and couldn't do a complete rewrite. Sure it's punishment, but I don't think he managed to convince them they did anything wrong. Coercion is much more important than lashing out with rough sex.