When you shutdown a server the players are kicked at the very end. This means that plugins etc are shutdown before the players are kicked/disconnected. This is not a problem when the server is operating normally since everything pretty much happens at once. However when there for some reason is a problem that causes the shutdown sequence to go slower (like a plugin problem), it will cause problems. The players are still online and this is when for instance items can get lost because the world and the player inventory is saved at different time and during the player is online. In other words it could cause items to duplicate or disrepair.

I would like to see that all players are kicked immediately before the shutdown sequence begin and that they will be unable to rejoin again before its been restarted. As noted this is not a problem when everything is working as it should, but it could (and have) caused problems when the sequence is delayed or halted.