This is an issue with Bukkit/Spigot sending corrupt clients and should obviously be reported there, but it is also a bit sad that this issue can cause a client crash. It seems that simple check would be adequate to catching this issue and not causing a crash. A specific example would be the client receiving multiple packets for removing a scoreboard due to a race condition on the server side, this commonly causes crashes on many servers, and it would be an easy fix for Mojang to implement.
(Crash Log: http://pastebin.com/uTY3p4rr)
Invalid. This is a modded problem and not vanilla as you said. This bug tracker is only for purely vanilla bugs.