If you receive an error in rtorrent such as No connection to rTorrent. Check if it is really running. Check $scgi_port and $scgi_host settings in config.php and scgi_port in rTorrent configuration file.
It appears your ruTorrent is not working as intended, but it is.
This is fixed easily by restarting rTorrent from your UCP.
There are many reasons why your rTorrent would crash such as running out of disk quota, deleting large torrents with the ..remove torrent .. with data plugin. Or even just overloading the client with active downloads.