Hannah had always known there was something weird about her boyfriend but a lot of other things clicked into place after she got hurt and had it confirmed that his hair was naturally green. She wasn't trying to be a conspiracy theorist or anything but there really was no other explanation that fit.
His difficulty with reading English. Not knowing what perfectly normal things were. His hair. Frequently saying humans were fragile as if he wasn't one. Never being able to see his family again.
He never specifically said they were dead. He said he would never see them again.
Little details like that kept coming back to the forefront of her mind until she was absolutely convinced. But what could she do about it?
When Hannah thought he was in Witness Protection, she figured he was so secretive as a matter of safety. That would be a lot more serious if he was an alien whose spaceship crash landed here with no way to return home.