Well I did some checking and it's pretty much as I thought.
Here's what NOAA put up on it's website about the fish.
"....NOAA Reminder on Atlantic Bluefin Tuna Regulations
November 22, 2011 - Recently, a New England groundfish vessel
incidentally caught an 881-pound bluefin tuna in a trawl net. 
At the dock, an officer with the Massachusetts Environmental Police conducted a routine boarding of the vessel. Knowing that
bluefin tuna are carefully monitored and regulated, the officer notified NOAA’s Office of Law Enforcement that a bluefin tuna had been caught....
NOAA’s Office of Law Enforcement examined whether the vessel’s permits allowed it to catch, retain or sell the fish. The vessel had an Atlantic Tunas General category permit, which allows it to catch bluefin tuna, but only by using handgear (such as rod and reel, handline, and harpoon).
There is no permit that allows bluefin tuna to be caught with trawl nets, even incidentally. Therefore, the vessel could not legally retain or possess this bluefin tuna.
This was explained, andthe fisherman was issued a written warning under the Atlantic Tunas Convention Act.The fisherman voluntarily abandoned the fish to federal law enforcement agents.
If a bluefin tuna is caught with fishing gear that is not authorized, even incidentally, the bluefin tuna must be released and cannot be retained....."
http://www.nmfs.noaa.gov/stories/2011/11/bluefin.htm
Like I said above all this stuff about the guy not knowing it was an illegal take are just B.S. He had to know that his permits were not valid for trawling up tuna. Sounds he brought it in thinking he could get away with pretending he caught it hook and line, and then got caught with the illegal fish in a routine inspection at the dock.
I'd say he's lucky he just got off with a warning.
Jim