All of these statements are true.
1. A hundred out of the 30+ thousand emails Hillary sent on her private server were marked "classified" after she had sent them. Therefore, Hillary could not have knowingly sent out or received such retroactively classified emails. Comey may have been right to chastise her for using a private server, but that's a different issue (and, as been noted by everyone except Republicans, Hillary's predecessor Colin Powell sent private emails, as did Condoleezza Rice's staff.
2. Three of the emails on Hillary's private server were indeed marked classified - but the markings on two were incorrect. So, in fact, these cannot be counted as classified emails that Hillary had on her private server.
3. The marking on the third was correct - on 1 out of more than 30,000 emails - but it was not listed at the top. So although Hillary did have that one classified email on her private server, it's reasonable to conclude that she did not know it was classified.
And that's it. No one is lying - neither Hillary Clinton nor the FBI Director. For some reason, the media today - including, unsurprisingly now, some of the geniuses at MSNBC, specifically Howard Fineman and Chris Cillizza - were saying that Hillary was not clear, was too defensive today, when she explained what happened. But, in fact, it's not the least bit unclear, and I'm finding the media opacity on this issue no help at all, to the point of not doing their jobs.