Views Bulk Operations execute php loop over reference values
For any field that has multiple values you can use field_get_items() to retrieve all values. For your specific case with the entity reference field, you'll need to retrieve the target_id property from each field item.

  $node = node_load($nid); //$nid is the node id you get from VBO
  $references = field_get_items('node', $node, 'field_MY_REFERENCE_FIELD'); 
  foreach($references as $index =&gt; $value) {
    $reference_nid = $value['target_id'];
    //@TODO: use $reference_nid to retrieve anything about referenced node
  }