It's also possible this commander is, as many are today, hyper-vigilant in protecting his own career.
Say the everyday typical student buffoonery happens, but this time it happens in a critical phase of flight requiring split second reaction time to correct it. Perhaps it's compounded by weather, gusty winds, com noise, etc. Metal gets bent and the CC is notified.
The CC sits down behind his desk and weighs his options:
"This IP made a mistake that any one of us can reasonably make with a bad student in poor conditions. I can call this IP in, lecture him, put him on a couple CT sorties, and perhaps have him give a squadron safety brief. I could go to bat for him at the OG and WG meetings. But metal was bent on my watch. What if it happens again? I'm going to get a lot of face time with the OG and WG over this and what if they think I didn't go far enough? If I give him a CC-directed Q3, it may be a little overkill, but then I have a high-vis corrective action paper-trail that I can wave around in the meetings letting them know that I'm an aggressive problem solver, and perhaps this won't affect my next assignment or chances for 0-6."