Professor Lessig explains on his blog what happened:
As you may have read me tweet, the organization that hosted me for this talk... [r]eceived a notice that Warner Music had objected to its being posted on copyright grounds. Apparently, YouTube's content-ID algorithm had found music in the video that they claimed ownership to. The organization is apparently responding by disputing the claim. I'll report back when I hear more.The key is Lessig's statement that "YouTube's content-ID algorithm had found music in the video." Here's what that means: YouTube employs an automated system for identifying music uploaded to its system. The major music companies, in cooperation with YouTube, have uploaded digital "fingerprints" of their songs to YouTube's content ID system (which uses AudibleMagic's technology). When a user uploads a video, the content ID system checks the music against the database of fingerprints, and applies a "business rule" set by the copyright owner: 1) block, 2) track, or 3) allow, and share revenue. Most major record labels participate and use option 3. WMG did so until late last year, when its agreement with YouTube broke down, and the setting for WMG's music flipped from "allow and share revenue" to "block."
So today, when a user posts WMG music to YouTube, its content ID system identifies it, blocks it from being displayed, and sends a notice to the user. At this point, the user can dispute the block through a simple online form. This is not the DMCA notice-and-takedown (and counternotice) process. Rather, it is a private system -- totally outside the DMCA -- that YouTube established to allow it to monetize videos (and mollify copyright owners, who are relieved of some of the burden of policing YouTube for infringing copies of their works).
So, assuming that Lessig accurately described what happened here (and I have no reason to doubt him), the video of his presentation was not the subject of a DMCA notice. (Indeed, Lessig's initial Twitter report did not claim this was a "DMCA" takedown.) Rather, the video was identified by YouTube's filter and blocked, and the copyright issue can probably be resolved by the poster (an organization that Lessig does not identify) taking 5 minutes to fill out an online dispute form. If, at that point, WMG still believes that the use of its song was infringing, it can then issue a true DMCA takedown notice (and, if necessary, the poster can file a DMCA counternotice).
As to the underlying issue: was Lessig's use of WMG's music a fair use? The problem I have in answering that question is that I'm not even sure which music triggered the video's removal. Lessig lists the music incorporated into his presentation, but the list makes no mention of WMG. (Was there simply a malfunction in the content ID system?) However, having watched the video, it does seem that Lessig used only brief excerpts of music to illustrate his arguments about "remix culture." In other words, probably fair uses (though, again, I'd want to know for sure which song was the subject of the claim before saying so for sure).
So what will happen? If the poster disputes the takedown through YouTube's system (which Lessig indicates is occurring), my guess is that WMG will not press the case, and the video will get re-posted. YouTube's content ID system isn't perfect, but it does have a feature that permits disputes like this to be resolved quickly, and without much hassle -- if that's what the parties actually want.
UPDATE: Lessig reports on his blog that "the protest filed by the uploader to the block was successful." Should be the end of the story.