Ironically enough though you pointed out a few of the not-so-badfic's punctuation errors, you made one of your own:

He wrote down a charge for glomping Haruka
You missed a period.

One more issue:
Miguel attached the Iwatobi-chan to the side of his backpack; no one in canon would bat an eye, and it might even stay attached when he dropped his disguise.
Since the next two clauses are explaining Miguel's action in the first clause, the semicolon should be a colon instead, signaling that an explanation was coming.

It happened to me twice now, so I have no other choice, but to bring this up here:

Why wasn't I informed that you were going to publish the mission? I didn't tell you I was done with my work.

Mind if I redirect you [HERE]?