Unfortunately i have very little to nothing to offer in terms of causality of this issue other than the fact that each time this has occured im told that the user was at an Enderman XP Farm in the end using a crossbow to shoot them, logs from the server provide nothing at all other than standard game output.
Once this does occur the game has frozen and after a short period all players are disconnected from the server and continually shown as still being online and a restart of the server after killing the PID form the server box itself resovles this issue.