// Declared a new function in NetworkListenThread
 public void closeConnections()
 {
     connections.clear();
 }

// Overridden it in IntegratedServerListenThread
@Override
 public void closeConnections()
 {
     netMemoryConnection.closeConnections();
     super.closeConnections();
 }

// Then added this on the bottom of stopServer in MinecraftServer
 if (this.getNetworkThread() != null)
 {
     this.getNetworkThread().closeConnections();
 }