Best we can tell the crew got picked on a bit, probably because he was the FO (mentioned by name in the letter).
They were listening to music during boarding, taxied "too fast" and used reverse during taxi, still listening to music during their pre-takeoff annoucement, threw the power forward on takeoff, among a few other miscellaenous things.
Now what really happened? Who knows. There was of course zero investigation or effort put into finding the right course, as is typical of anything C5'ish. Several things didn't make sense about the story.
Either way, TM went on this little rant against the Colgan Capt (training Capt from what we hear) and had all these stickers made and what not.
It's all pretty childish in the end. I'd rather have any Colgan guy on my JS than Timmeh.