He was very, very careful in his phrasing (and then large on hyperbole) with what he stated. He claimed two emails carried 'confidential markings' (which was only sorta true) and then switched gears on confidential emails (which is, in fact different). There are maybe 30-40 emails that were sent that had confidential or higher (most were just confidential). So about .006% error rate on humans using email and sent something through email they shouldn't have.
One of the confidential emails... was to a lawyer and "confidential" in the sense that lawyer-client privileges applied. There were a couple of (C) markings in a few emails, but the top actually didn't have the markings for Confidential/Secret or whatnot. An incredibly huge percentage of emails were marked confidential expo-facto (and by other agencies that tend to try and classify _everything_, including public knowledge of the weather at times).
James Comey just did a public hatchet job of "selling" that Hillary should have been indicted, then basically admitted he didn't have a case that any competent prosecutor would attempt to take before a judge. Congrats, partisan hack, you pulled the wool over most of the viewers and readers.