It appears the basis for the takedown is that the distribution includes code that is in violation of the license. Specifically, Bukkit includes code that is not GPL licensed. The GPL prohibits this, and so the author is able to exercise his rights under the GPL. To restate it more concisely, the claim made is that the code authored by the DMCA issuer is being distributed in violation of the license under which it was written (the GPL).

What makes this extraordinarily messy is the fact that it is almost indisputable that the author was aware of this at the time he contributed. IANAL, so I don't know how that effects the license, but entering in to agreements that you are knowingly violating at the moment you enter them has the effect of providing a basis to challenge the validity of the agreement. Again, IANAL, but my concern would be that if the license were found null and void, the whole situation would fall back to copyright law, which still gives the author ownership of the code he has written, because there was no explicit assignment of copyright.

Basically, the choice of GPL for the Bukkit project was a timebomb from day one. Any project using the GPL would be wise to take note of what has happened here. Should someone find any significant amount of proprietary code in your GPL project, they can quite simply nuke your entire project with a single DMCA.