Hillary Clinton was being investigated for using her personal basement server to handle official emails containing classified or confidential information. Something which, if I had done it when I had a security clearance, I would have been not only fired on the spot, but escorted off the facility in handcuffs for doing.
Anyone can put classified information into your email account by forwarding the right news story or Wikipedia page to you in an email. There is a lot of classified information that is also publicly known. Federal law enforcement understands this and takes it into account when deciding to prosecute.
Note that Hillary Clinton was not prosecuted despite the subsequent administration basically running on a promise to do so.
Official business with classified information is never done via email, even if everyone is using the government email servers. There are separate networks, devices, and protocols for storing and operating with classified information.
Also, as has been said repeatedly, the US government doesn’t have a binary “classified” or “not classified”. There are many different levels and administrations introduce/adapt them as necessary[1], and there is a practice of retroactive classification.
