D7 entity references don't migrate straight-forwardly

File core/modules/migrate/src/Plugin/migrate/id_map/Sql.php edited to add drush_print_r for profiling purposes.

  /**
   * {@inheritdoc}
   */
  public function lookupDestinationId(array $source_id_values) {
    $results = $this->lookupDestinationIds($source_id_values);
    drush_print_r('lookupDestinationId');
    drush_print_r('$results');
    drush_print_r($results);
    return $results ? reset($results) : array();
  }

  /**
   * {@inheritdoc}
   */
  public function lookupDestinationIds(array $source_id_values) {
    drush_print_r('lookupDestinationIds begin');
    drush_print_r('$source_id_values');
    drush_print_r($source_id_values);
    if (empty($source_id_values)) {
      return array();
    }
    // Canonicalize the keys into a hash of DB-field => value.
    $is_associative = !isset($source_id_values[0]);
    $conditions = [];
    foreach ($this->sourceIdFields() as $field_name => $db_field) {
      drush_print_r('lookupDestinationIds inside foreach');
      drush_print_r('$field_name');
      drush_print_r($field_name);
      drush_print_r('$db_field');
      drush_print_r($db_field);
      if ($is_associative) {
        // Associative $source_id_values can have fields out of order.
        if (isset($source_id_values[$field_name])) {
          $conditions[$db_field] = $source_id_values[$field_name];
          unset($source_id_values[$field_name]);
        }
      }
      else {
        // For non-associative $source_id_values, we assume they're the first
        // few fields.
        if (empty($source_id_values)) {
          break;
        }
        $conditions[$db_field] = array_shift($source_id_values);
      }
    }
    drush_print_r('lookupDestinationIds after conditions');
    drush_print_r('$source_id_values');
    drush_print_r($source_id_values);
    drush_print_r('$this->sourceIdFields()');
    drush_print_r($this->sourceIdFields());
    drush_print_r('$conditions');
    drush_print_r($conditions);
    drush_print_r('$this->getSourceIDsHash(array_values($conditions))');
    drush_print_r($this->getSourceIDsHash(array_values($conditions)));
    if (!empty($source_id_values)) {
      throw new MigrateException("Extra unknown items in source IDs");
    }

    $query = $this->getDatabase()->select($this->mapTableName(), 'map')
      ->fields('map', $this->destinationIdFields());
    if (count($this->sourceIdFields()) === count($conditions)) {
      // Optimization: Use the primary key.
      $query->condition(self::SOURCE_IDS_HASH, $this->getSourceIDsHash(array_values($conditions)));
    }
    else {
      foreach ($conditions as $db_field => $value) {
        $query->condition($db_field, $value);
      }
    }
    drush_print_r('get-query');
    drush_print_r($query->__toString());
    return $query->execute()->fetchAll(\PDO::FETCH_NUM);
  }

Error Run Screenshot

✝ vagrant@multi-vlad ✝ ../site/vlad_aux/d7d8-dev
$ drush ms
 Group: ya_example  Status  Total  Imported  Unprocessed  Last imported       
 d6_file            Idle    34     34        0            2016-09-16 16:40:23 
 ya_user_role       Idle    4      4         0            2016-09-16 16:40:33 
 ya_user            Idle    2      2         0            2016-09-16 16:40:40 
 ya_node_page       Idle    10     10        0            2016-09-16 16:40:48 
 ya_node_article    Idle    8      1         6            2016-09-16 17:15:34

✝ vagrant@multi-vlad ✝ ../site/vlad_aux/d7d8-dev
$ drush mi ya_node_article --limit=1
lookupDestinationIds begin
$source_id_values
Array
(
    [target_id] => 75
)

lookupDestinationIds inside foreach
$field_name
nid
$db_field
sourceid1
lookupDestinationIds after conditions
$source_id_values
Array
(
    [target_id] => 75
)

$this->sourceIdFields()
Array
(
    [nid] => sourceid1
)

$conditions
Array
(
)

$this->getSourceIDsHash(array_values($conditions))
02db060eff943c9d3e99f79dd573e1e2ab0d52d4dd041f59a0bc63f453f0af82
Processed 1 item (0 created, 0 updated, 1 failed, 0 ignored) - done with 'ya_node_article'                                          [status]

✝ vagrant@multi-vlad ✝ ../site/vlad_aux/d7d8-dev
$ drush mmsg ya_node_article
 source_ids_hash                                                   level   message                           
 33c8981f3a32ae575f410557a535f68eead82c0d3535cbfa5025bb9658e93d64  1       Extra unknown items in source IDs 
 09b17db9613247d1118449fda0033fa7449d0cd5a1b6456dbfbcfb2bd66ff196  1       Extra unknown items in source IDs

✝ vagrant@multi-vlad ✝ ../site/vlad_aux/d7d8-dev

✝ vagrant@multi-vlad ✝ ../site/vlad_aux/d7d8-dev
$ drupal config:debug migrate_plus.migration.ya_node_article
 migrate_plus.migration.ya_node_article 
 langcode: en                           
 status: true                           
 dependencies: {  }                     
 id: ya_node_article                    
 migration_tags: null                   
 migration_group: ya_example            
 label: 'Nodes (Article)'               
 source:                                
   plugin: d7_node                      
   node_type: article                   
 process:                               
   nid: nid                             
   vid: vid                             
   langcode:                            
     plugin: default_value              
     source: language                   
     default_value: und                 
   title: title                         
   uid: node_uid                        
   status: status                       
   created: created                     
   changed: changed                     
   promote: promote                     
   sticky: sticky                       
   revision_uid: revision_uid           
   revision_log: log                    
   revision_timestamp: timestamp        
   body: body                           
   field_drupal8_pages:                 
     plugin: migration                  
     migration: ya_node_page            
     source: field_drupal7_pages        
 destination:                           
   plugin: 'entity:node'                
   default_bundle: article              
 migration_dependencies:                
   required:                            
     - ya_node_page     

@mikeryan
Thanks mike! I will update the drupal 8 migration api community documentation cookbook to include this tip.

I am closing this issue because although the fix does not technically tackle the fail

  field_drupal8_pages:
    plugin: migration
    migration: ya_node_page
    source: field_drupal7_pages

The fix is a workaround through :

  field_drupal8_pages:
    plugin: iterator
    source: field_drupal7_pages
    process:
      target_id:
        plugin: migration
        migration: ya_node_page
        source: target_id

This is good enough. The actual fix should be another issue.