I think the Justice Department is saying you asked for proof of residency by asking for green cards from suspected aliens but did not ask for a SS card, passport, or birth certificate from those you assumed were citizens.
More than that...you can’t require a green card from foreigners who want to make pizza. I might be wrong but I think I have only seen such a requirement in the defence industry. The business owner is clueless about the wide array of work permits in the US.