After the hack, in Chapter 44, Kestrel, Dent, and The MIND are discussing who could be responsible for the parameter test, and, to a greater degree, whoever hacked the SCT. When they offer up the possibility of "a rogue element in the hierarchy", I can't help but wonder if the one responsible is General Shira Able.

I know it might be a stretch, but hear me out. She's got means, motive, and opportunity. Her position alone gives her access, and she's already given orders to mess with Rei's SCT's (and by extension his growth, in a way). She also might hold a grudge against Rei from the way her shitstain nephew acted durring the assignment exam. Maybe she thinks "fuck this kid, he indirectly embarrassed my nephew and me by extension because he got the device and not my shitstain nibbling." (Paraphrasing).

It's not like we haven't seen others (Reese) in positions of power abuse it. Sure, she could use any excuse, people often do in Politics and it'd be pretty easy to spin it as "We don't have time to cuddle them, he's got S rank growth, let's find out what that means and make him grow as fast as possible because we are actually pretty fucked on the war front with the archons", assuming that Kestrel and The Mind were right about that and assuming General Abel knows that as well.

Also, I get the feeling she's not liked at all because she's an over ranked twatwaffle that is honestly really good at her job just lacks actual human ethics.