From what I heard it was a paperwork issue with the MEL procedures for something on the airplane. Honestly, there are a lot of grey areas in the MEL books that can lead one down the wrong road and can get one in trouble. What exacerbated the situation for the GoJet Pilots was the FAA POI for GoJets, was a former TSA Pilot and that made him go after them with a little bit of vengeance.
I would say that MAYBE 5% of pilots at anyone airline would get a FAA Violation while employed at that airline. Even that number would be a tad high I would say as well.