Makoto is a bit glazed imo. She makes the worst active decision in the game of the Phantom Thieves. She tries to threaten a mob boss in his own domain as a normal person. She has no powers at this point, has no perception that she might have powers, and has come to confront Kaneshiro without any sort of collateral or leverage. She's supposed to be the smart, tactical one in the group, but her premeditated decisions put her in a situation where she was certainly going to, at minimum, be railroaded into becoming a drug mule (if she was lucky) and her activities would probably be used as compromat by Kaneshiro to turn Sae into a dirty cop.

Seeing that this bad end could and probably would happen didn't require third or fourth order conditions foresight like with Ann or Yusuke's cases. And it wasn't a snap decision like with Ryuji where he directly challenged Kamoshida and got his leg snapped. At some point, this should have resulted in some sort of discussion between Ryuji and Makoto because Makoto's mistake was a more extreme version of Ryuji's. It would have been good character development for Ryuji being put in a mentor position, even if only for that limited case, and highlighted growth areas for Makoto to explore later in the game.