How do I get multiple references from the autocomplete?
The comma is used to separate multiple references, but looking at the code in Name::valueForm() I would say the form element needs to use a property more.

  $form['value'] = array(
    '#type' =&gt; 'entity_autocomplete',
    '#title' =&gt; $this-&gt;t('Usernames'),
    '#description' =&gt; $this-&gt;t('Enter a comma separated list of user names.'),
    '#target_type' =&gt; 'user',
    '#tags' =&gt; TRUE,
    '#default_value' =&gt; $default_value,
    '#process_default_value' =&gt; $this-&gt;isExposed(),
  );


Settings #tags to TRUE makes the the form element accept multiple values.

The format of the values assigned to the form element is evident in EntityAutocomplete::validateEntityAutocomplete() (its validation handler), which uses this code.

  $input_values = $element['#tags'] ? Tags::explode($element['#value']) : array($element['#value']);

  foreach ($input_values as $input) {
    $match = static::extractEntityIdFromAutocompleteInput($input);
    if ($match === NULL) {
      // Try to get a match from the input string when the user didn't use
      // the autocomplete but filled in a value manually.
      $match = static::matchEntityByTitle($handler, $input, $element, $form_state, !$autocreate);
    }

    if ($match !== NULL) {
      $value[] = array(
        'target_id' =&gt; $match,
      );
    }
    elseif ($autocreate) {
      /** @var \Drupal\Core\Entity\EntityReferenceSelection\SelectionWithAutocreateInterface $handler */
      // Auto-create item. See an example of how this is handled in
      // \Drupal\Core\Field\Plugin\Field\FieldType\EntityReferenceItem::presave().
      $value[] = array(
        'entity' =&gt; $handler-&gt;createNewEntity($element['#target_type'], $element['#autocreate']['bundle'], $input, $element['#autocreate']['uid']),
      );
    }


The form element value is an array of item whose target_id key is an object of the requested entity.

(From that code, it is also clear that #tags makes the form element accepts multiple references separated by commas.) 

As for the using reference that aren't found, you can decide what the autocomplete does by setting #validate_reference: If you set it to TRUE, and #autocreate is not set to TRUE, the autocomplete will accept only existing references.