I would say you are overriding it in the wrong location. Rather than attempting to override the actual method, in the template, use this
$notes = apply_filters( 'cn_output_notes', $entry->getNotes() ); method instead and wrap the output in your own
div with whatever class you wish.
Just make sure you put your template override file in one for the locations specified in the tutorial so it is update safe.
Hope that helps!