If you allow multiple values in the reference filter settings and allow your "View used to select the entities" to have multiple arguments and your "Arguments for the view" is a multiselect filter, then this possibility gets destroyed in entityreference_filter_view_result.inc in line 266:
$args[$i] = current($args[$i]);

Instead of this a
$args[$i] = implode(',', $args[$i]);

would solve this issue and allow the transport of multiple args between the views. Is it possible to fix this or what is the reason behind the current implementation?