If like me you want to know what the "procedural mistakes" were, and not read what is almost certainly someone's unnecessary diatribe about why the end result is wrong (hint: it's wrong, so, so wrong, and we all know why), let me help you find them. Use the last link in the summary, copied here:
Summary: The case is about whether Lavabit should have been held in contempt, which hinges upon whether the court had the right to demand what it was demanding. However, Levison did not make any legal argument against the demand at the time. Therefore, it was justifiably held in contempt. The issue of whether the court had the right to demand private keys is important, but the issue needed to be raised sooner and with more force. Now it's irrelevant to further proceedings.
I am not a lawyer and I have not actually finished reading the article yet.