There's not a lot of context in the take-down notice... does anyone know the actual story? http://dl.bukkit.org/dmca/notification.txt
It consists of two major projects. Bukkit itself is an API that plugin authors code against. In theory it could be implemented for e.g. Terraria too but in practice its completely tied to Minecraft. Bukkit (the api) is licensed under GPL with little issue.
CraftBukkit is the implementation of this API. It is licensed under LGPL.
This was originally started as a community project. However the issue is that CraftBukkit includes a decompiled Minecraft server, which mojang never officially allowed.
This meant that Bukkit (the server) contained the bukkit api (GPL), the craftbukkit implementation (LGPL) and the Minecraft server ( All rights reserved) and was being distributed as "GPL". While mojang looked the other way about their proprietary software being distributed as GPL, everyone was pretty much happy.
The issue gets muddier when Mojang hired the core Bukkit devs to work on Minecraft. They left the Bukkit project to run itself and everything continued as is for two years.
Then two years later the community team announce they're shutting down the project. At this point, Mojang reveals that when they hired the original team, they also acquired the Bukkit project (trademarks, infrastructure, the original core teams code, etc) and as such it didn't belong to the current community team to shut down.
Now one of the GPL contributors is demanding that Mojang take down the project because it contains his code under the GPL but isn't validly licensed under the GPL due to containing the all rights reserved mojang code.