It's not a question of looking for the holes in the story. In order to feel a story deeply, I play the role of MC in my head. For instance, when he acts as a naive sucker, I imagine how should he act, what should he say. Experiencing novels that way, you actually get some experience related to those situations. It's educational and it's enhancing the immersion. And yes, sometimes the stretch, the gap between how it should be and how it was done becomes uncomfortably big.
PS. As for superpowers adversaries, while you have all the resources of the government, well...
PPS. And the position "Let's not try to touch them, as they can be too powerful", doesn't seem to be reasonable.
And I think it was not known at the time that there were power users among the adversaries. Didn't Haruka say that the only known users were MC and his "sisters"?
And even if it was a rescue operation behind enemy lines, why not shoot to kill?
All that would make me hard to believe that it was not just a show, if I was MC.