There is a difference between not wanting to stand and telling someone the flag is racist against black people. That's likely what set the substitute off especially since it sounds like she's a cuban refugee.
That said why in the hell was he sent to juvie instead of just going to the principal's office that's weird and dumb. And likely a slam dunk if they decide to sue the district. I would like to know if there is more to this story because I don't think you can send someone to juvie for not standing for the pledge.
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The word of an adult is going to beat that of an 11 year old 100 percent of the time unless it's involving violence of some sort against the child. But yes if an adult takes the stand and the oath and then swears that the child did threaten them with physical violence it will absolutely beat the word of an 11 year old. I said a lot of stupid shit when I was 11 and if I had the cops called on me for it you can bet I would have lied my ass off about it of course I never threatened to beat people up but talking about how adults were idiots and that kind of stuff definitely did that. What was left out of the op is the claim that he would commit physical violence that's why the cops were called.