The whole sequence with Dan, Shindo and Detective Kurosawa in the basement of the Amada building. Three humans vs HUNDREDS of zombie-like defective Hollow Children. Considering they're rejected/defective versions of robots who believe themselves to be human, it's quite possible they have the mentality of a rejected/defective human. That is to say, they're homicidally insane.
Hollow Children are the ultimate infiltration agents - and they could be anywhere. Given that one Hollow Child became Chairman of the Joint Chiefs of Staff - it passed all the background checks and vetting that needed to take place - you can't be sure you're not surrounded by them.
Surrounded by them? For all you know, you could be one.
Forget the fact that he's a crazy Beta Test Baddie who is responsible for all the horror relating to Hollow Children by virtue of being their creator, what's really scary about the Amada AI is what was done to him. Imagine how you'd turn out if your "father" essentially tortured you from birth.
Hollow Children look the same as humans. How can you be sure the main characters aren't Hollow Children themselves? Granted, the Amada AI doesn't control them, but maybe it's because it isn't trying to.
How about the idea that the little fact that your mother was a Hollow Child is considered reason enough to send heavily armed military crews to hunt you down and kill you?