My understanding of the issue makes things look better for Wolfe.
He contributed code to the project - licensed as LGPL - before the Bukkit team was aquired by Mojang. At that time the server code - decompiled and deobfuscated - included in the releases was not falling under the LGPL license because it was not owned by the releasing team.
Forward to when the Bukkit team is aquired by Mojang - who owns the copyrights to the server code - and a new release is made. At this point the server code included in the release, which is copyrighted by Mojang, falls under the LGPL.
I am not saying that this is what's the legal reality of the case, but I think this is what Wolfe thinks and why he issued th DMCA takedown notice.