A number of people are saying the same thing, but I'll just respond here.
>The only time this would be a problem is if the bootleg trailer were uploaded before they uploaded the ContentID data, and Fox wanted to then upload the ContentID data and have it removed automatically. I can't see why they would do this, however, since presumably they are reacting to the bootleg upload in this case, and can then simpply issue a manual takedown request.
Fox can issue a manual takedown, but they shouldn't need to. That's the entire point of the deal Youtube cut with the major studios that created ContentID. Fox uploads the videos they own, and then Youtube/ContentID finds all the infringers so that Fox doesn't have to pay a person to do it themselves.
This issue is obviously a special case where a clip from a video game, apparently sourced from Youtube, was excerpted in a network TV show. The network TV show - which is obviously protected - set off ContentID flags. Fox didn't set out to upload a Double Dribble clip to ContentID. This is an edge case.
The article then spuriously goes on to about the DMCA, but there's no evidence presented any DMCA takedown whatsoever. I don't even see any evidence of human intervention at all. If I had to guess, there's a setting in Fox's ContentID: If from Family Guy, block entirely.
It's unfortunate that this happened. It shouldn't have happened, but this is what inevitably happens when a technical solution (ContentID) is used to solve a social problem (piracy).
There should be an easy remedy for the video creator, and he is free to pursue copyright charges against Family Guy for using his video game clip in a TV show, if he thinks he has the rights to that clip. (I have no clue on that one.)
But this is a mountain being made of a molehill. Nobody's rights are being infringed. This is the deal you make when you sign on with Youtube: the big studios have the most power. They're only one player; if this deal irks you (and there are definitely legitimate reasons it would) there are plenty of other ways to host video.