I had a similar thing happen on JFK-DFW flight a few years back. The guy sitting next to me had "stolen" his upgrade to first class by being one of the last to board and he just took an empty seat in first. About 1.5 hours after take off the flight attendant questioned him about it and I overhead her say he was actually assigned a seat towards the back of the plane. He was told to keep his seat but upon arrival at DFW two armed and uniformed police officers boarded the plane and took him away for what I assume became an unpleasant interview.

I never understood how he was not discovered prior to departure since they usually take a passenger count.