Custom checkout pane for order comments not saving
This was fixed by passing ['order_notes'] into $values.

 /**
   * {@inheritdoc}
   */
  public function submitPaneForm(array &amp;$pane_form, FormStateInterface $form_state, array &amp;$complete_form) {
    $values = $form_state-&gt;getValue($pane_form['#parents']);
    $this-&gt;order-&gt;set('field_order_notes', $values['order_notes']);
  }