Midori knew it before he even knew what they were -- the unreal, human-but-not-quite-natural state in which they existed. They had all the makings of real people, but they were missing a key element, and that frayed thread led to the unravelling of others until they were more than machines but less than whole souls. Zero-sum: when you add up the negatives and positives, there's nothing left. Removed just so from the rest of their species (though not their peers, never their peers, because the Zeroes are peerless, aloof and alone) that they don't have to follow its rules.
He first realized just how different they were when Ai ran in and huddled herself in his arms, her forehead smudged with slick red. She clung to him, a fearless girl trembling in the wake of something even she could not look at with an unblinking eye.
"He threw a rock at you?" asked Midori when she had explained. It was almost too strange to believe, but there was the blood, and Ai wouldn't lie about it. 'We're supposed to be above this,' he thought. 'Physical fighting is base and deplorable. It's almost against our nature.'
And that was when he first realized that the nature of the Zeros is not anything like the rest of theirs -- nothing like human nature at all.