Well, first, i'll put the same disclaimer that says the cuffs and taking him in was over done.
But with more context, apparently the kid was in trouble/suspended a ton. He had gotten in trouble for creating some thing where he could turn the teacher's projector on and off when he wanted, which by the way, is a fantastic prank lol. The clock he also "made" was supposedly just a regular clock that he took the face off of and put in a separate case. He was also told repeatedly bo other teachers to put the clock away, and he didn't.
So, the media made him out to be the adorable, innocent kid. Again, not knowing what is so, it sounds like he may have actually been quite the troublemaker.
But the crux of your argument, as I recall, was basically that teachers should just magically know the difference between a homemade bomb and a homemade clock, seems logical.
