There's a fundamental misunderstanding about classified material, which is that it becomes de-classified once it is public. Not true.

For example, take the Wikileaks information dump, which came from a huge cache of State Dept. cables and has now been covered in hundreds of public newspaper articles. If one of her friends forwarded one of those articles to Clinton, boom, she now has classified information in her email. Why? Because those cables, despite being leaked, were never de-classified.

Another example: a lot of the stuff revealed by Snowden was classified at a very high level. It still is today, even though it is widely available public information. Can you see how this could cause problems for someone who is a government official, but has friends/family/contacts who wish to discuss these news articles?

The press is a well-known vector that leads to a lot of government staff having classified information in their unclassified email systems. Typically investigations are rare and prosecutions rarer, because it's basically impossible to prevent and does no practical damage (since the info is already out there).

This is why the mere fact of having classified material on an email server does not necessarily imply incompetence or malice.