Initially, she claimed there was no classified information on the server at any time. Further, when she was required to turn over records to comply with archival rules, she had her staff delete the personal messages and pass the rest along.
In the current investigation, they've discovered classified emails - some classified after the fact, some not - which included KH-designated intelligence (aka detailed satellite images). In addition, when she delivered the data to the State Department, she gave a copy of all of it to her lawyer, who didn't have clearance for the classified data.. which shouldn't have been there anyway.
Yes, previous Cabinet-level staff had used private servers but the National Archives explicitly recommended against it in 2006 (a recommendation, not law) and then President Obama signed an Executive Order making it the law in 2009. Secretary Clinton continued doing it until she left the State Department in 2013.
At minimum, it was disregard for the recommendations and eventual law. At worse, it was flagrant disregard for protecting the means and methods - that includes people - who collected and needed that information.