How is a machine crying?
Maybe they are actual human bodies with mechanical brains? we don't know where exactly the bodies go yet. Maybe they save them to reprogram them. The MC did offer the old lady a new software inside the girl, after all.
Just brainwashed people. Brawinwashing lasts only for so much time so they have to be retrieved before it fails and they could reveal the truth behind their existence.
Or something like that.
Probably by using 3 advanced simulative modules that acts as Ego, Id and SuperEgo
Do you even AM?
They're machined designed to be as human-like as possible. Crying is one of the most integral forms of behaviour to signalize sadness.
It'd be pretty stupid to not give them the ability to simulate crying.