The AC: Brotherhood soundtrack was uploaded to Demonoid more than four months ago by a member named "arsa13". The same user is credited for encoding the official soundtrack's MP3s (see the screenshots below). "Apple Chamber" is the only song that doesn't mention arsa13, but that track was also excluded from the original torrent file.
This, of course, is ironic given the developer's stance against piracy and torrent sites. Last year the company introduced a new DRM scheme in the name of piracy that requires users to remain online while playing. To the dismay of fans, the mechanism has been used in Assassin's Creed II, The Settlers VII, Splinter Cell: Conviction and other titles.
This is the second time Ubisoft has been caught using torrented content. In 2008, customers who bought a digital copy of Rainbow Six: Vegas 2 couldn't launch the game after installing an official update. Ubisoft resolved the issue with a second patch, which was eventually discovered to be a torrented No-CD crack from warez group RELOADED.
We should note that this story first surfaced on Wednesday and Ubisoft hasn't released a public statement besides telling Eurogamer that it's investigating the matter. It shouldn't take more than 48 hours to determine if Brotherhood's retail soundtrack is from a legitimate internal source, so we're not sure what to make of the company's silence.