Re: Do not understand the issue
There's three parts to it. First there's the fact she was running her own email server, which may or may not have been secure, which almost certainly handled correspondence which was classified. This isn't a major issue as previous Secretaries of State have done the same.
Second is that she, or people in her employ, seem to have used that email server to bypass the Freedom of Information Act by pretending it didn't exist and so the emails couldn't be produced. This is pretty questionable, and if it's the case and was discovered earlier would likely have resulted in serious fines for her department
Last part is that she apparently sent on documents which were classified to people without clearance and stored them on the server which may or may not have been secured. Really this is what the Department of Justice is interested in, because if it turns out the documents were classified before she got them then she may be facing criminal charges. It's all kind of complicated though because they may not have been classified yet when she got them and she may not have been notified of them being classified after the fact, so there's the question of whether she should have been able to anticipate whether the documents would have been classified or not and whether she can be held liable for publishing documents which she knew *would* be classified but haven't been rated as classified *yet*
Basically it's a clusterfuck of bad document management but is unlikely to result in criminal charges, whether because there was no crime committed or because it would be so difficult to prove, but might impact her as a presidential candidate if she gets the nomination for the Democrats regardless because it's a pretty easy bit of mud to sling