This error occurs on shutdown (stop) on both Windows and CentOS linux vanilla Minecraft servers. I have noticed it since the 1.4 pre-release. It causes no issues to game play obviously since it only occurs on shutdown.
I am including my start up scripts, command line outputs and server.logs in a single file as an attachment.
Reinstalling Java did not correct the issue on either system.
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So when you type /stop does this happen? if your not typing /stop, then its not a bug.
Yes. This occurs when typing stop on both the linux server and windows server as I said above. From within the game and from console.

Ok, just checking.
This will happen if the port is closed without sending the clients a disconnect packet first. This isn't really a bug and can occur naturally if the server isn't shut down fully.
Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.