Server slowly dies on Ctrl+C

[NorbiPeti]

Describe the bug
The server seems to slowly disable each plugin and shut down with minutes in-between. The whole shutdown process took almost 20 minutes.

To Reproduce
Steps to reproduce the behavior:

1. Press Ctrl+C

Expected behavior
The server runner shuts down, maybe the server as well, but finishes in a few minutes.

Events
22:25:15 Server starts to stop (Ctrl+C is pressed on console), Jobs and Towny shut down (and probably ButtonChat), Disabling <plugin> messages don't appear from the plugin manager
22:25:20 First message sent that indicates that the chat plugin is disabled
22:27:34 Dynmap is disabled as well
22:39:51 Essentials is still working, based on the commands ran by the players (/tpahere, /tpaccept)
22:41:38 FAWE still seems to be running (WE command ran, assuming successfully)
22:42:09 All DB transactions during this session are being validated (This may take a while if corrections need to be made) from Thread-2 (which seems to be the Server shutdown thread), Discord exception from the same thread: changePresence failed because the bot's not logged in - while disabling DiscordPlugin
22:42:09 ButtonCore is disabled
22:42:10 The MC server is turned off (Saving players), players are kicked with Server closed
22:42:10 A ConcurrentModificationException occurs while disconnecting a player

[22:42:10] [Thread-2/WARN]: Exception in thread "Thread-2" 
[22:42:10] [Thread-2/WARN]: java.util.ConcurrentModificationException
[22:42:10] [Thread-2/WARN]: 	at java.util.HashMap$HashIterator.nextNode(HashMap.java:1442)
[22:42:10] [Thread-2/WARN]: 	at java.util.HashMap$KeyIterator.next(HashMap.java:1466)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.EntityTracker.untrackEntity(EntityTracker.java:160)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.WorldManager.b(WorldManager.java:29)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.World.c(World.java:1101)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.WorldServer.c(WorldServer.java:1182)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.World.kill(World.java:1138)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.PlayerList.disconnect(PlayerList.java:431)
[22:42:10] [Thread-2/WARN]: 	at buttondevteam.discordplugin.PlayerListWatcher.disconnect(PlayerListWatcher.java:166)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.PlayerConnection.a(PlayerConnection.java:1102)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.PlayerConnection.disconnect(PlayerConnection.java:260)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.PlayerList.u(PlayerList.java:1334)
[22:42:10] [Thread-2/WARN]: 	at buttondevteam.discordplugin.PlayerListWatcher.u(PlayerListWatcher.java:338)
[22:42:10] [Thread-2/WARN]: 	at net.minecraft.server.v1_12_R1.MinecraftServer.stop(MinecraftServer.java:475)
[22:42:10] [Thread-2/WARN]: 	at org.bukkit.craftbukkit.v1_12_R1.util.ServerShutdownThread.run(ServerShutdownThread.java:17)

[NorbiPeti]

The shutdown indeed propagated to the server itself, Thread-2 is a shutdown hook registered by Spigot/Bukkit. The cause of the slowdown is unknown.