If a very verbal (often too verbal) 12 year old child on the autism spectrum has trouble speaking appropriately and particularly likes to say a bracha when he wants to and not necessarily when it's needed (e.g., he very clearly knows that you don't generally say a bracha on food eaten in the course of a meal where you've said hamotzi on bread, yet he often insists on saying a bracha anyway) and then gets very upset when others don't say amen because is was an unnecessary bracha, should those who hear the bracha say amen anyway? Is it correct that you don't say amen if a bracha wasn't supposed to be said?
The Shulchan Aruch writes (OC 215:4):
כל המברך ברכה שאינה צריכה הרי זה נושא שם שמים לשוא, והרי הוא כנשבע לשוא ואסור לענות אחריו אמן.
Anyone who says an unnecessary blessing has taken God's name in vain and it is forbidden to recite Amen after him.
So it would seem that you are correct in not saying Amen.
As for the educational/parenting aspects, I don't think a definitive general rule can be given, but I think that responding 'Amem' instead will often succeed at calming the child, although that benefit needs to be balanced against the fact that it may come off as encouraging this 'bad' behavior. CYLOR and CYLCP.