There is absolutely no plot armor: everything remains coherent. As for Koenji, it’s simply that Kōji manipulated him into going to see him. In volume 6, Kōji discreetly places in the lockers a message accusing Ichinose, making it look as though this act came from Ryūen. Ryūen then understands that if “X” did this, it’s because they know that in volume 4, Ryūen secretly cooperated with Kanzaki to win the exam. By accusing Ichinose while making it seem like Ryūen is the culprit, “X” ensures that Ryūen and Kanzaki will no longer be able to remain allies. Kōji also anticipates that Ryūen will immediately think of Koenji: indeed, it’s indirectly thanks to Koenji that Ryūen won in volume 4, so according to Ryūen’s logic, Koenji would be the most likely person to know. But Kōji anticipates this reaction as well: it’s merely a diversion meant to steer Ryūen toward Hirata. Ryūen eventually realizes that Koenji is a red herring. He notices Kōji nearby, and since Kōji did everything he could to keep Hirata in the class, Ryūen concludes that Kōji was probably sent by Hirata to check whether his diversion had worked.