Can someone explain what happened in tonight's Dr Who (The Almost People)?

Okay, am I the only one who really, really didn't get that? Normally I manage to understand whats going on (kind of) but I am majorly confused. I left the room for like a second- came back in Amy's 'not real' she gets vaporised and is now having a baby? How do they know she isn't real- what exactly happened there? Could someone explain- thankyou <3