Just doing /kick Notch without a reason will always kick the player with shortest name apparently.

Difficult to test honestly, don't want to kick players who shouldn't be.
But it sure seems that way. No matter which name you type, once I connect with account name "DDR", he gets kicked.

Are you on Spigot 1.9 or 1.10?

1.9

Is it always the shortest name, regardless of if that name matches at all?

I was able to reproduce this. Something to do with getPlayer(String). I don't recall it behaving like that.