It bugged me that they had Bernard already working as Lupo's partner without explanation. I thought it would take a while for him to earn that position. I mean, just last week he played a role in Green's departure, so just dropping him into Green's job right away feels kind of ghoulish. Sure, he turned around and helped clear Green last week, but still, that doesn't seem like enough.
And for an episode based on Scientology, it ended up being kind of wishy-washy, not being willing to paint the "Systemotics" cult in too bad a light, and painting its critics as paranoids and opportunists.
Also, it had kind of a formulaic feel: a problem arises with the case, Cutter is stymied and upset, Jack offers words of wisdom that solve Cutter's problem, lather, rinse, repeat.
And when Cutter did come up with his own tactic at the end, exploiting the guy's paranoia to wring a confession out of him, that was just about the most sleazy and unethical thing I've ever seen a prosecutor do on this show, and with McCoy's record, that's saying something. He terrorized that man into accepting a plea, and the fact that the source of terror was the man's irrational fear doesn't make that any less a violation of the defendant's rights and of the integrity of the system. Surely the defense lawyer could've gotten the confession thrown out? I don't find it believable that he caved in so easily.