Shut down my Spigot server for an update. Not everyone was disconnected at the same time or with the shutdown restart message set in spigot.yml. Some users had the restart message sent to their client, some users had an IOException string, and some users had the BungeeCord '[Proxy] Lost connection to server message'.

http://paste.ubuntu.com/10440902/

BungeeCord dev 1050
Spigot compilation as of 02/26/14.

I've been experiencing this issue for a while now.