drupal_set_message on node edit page shows twice with theme hook
Form alter changes the form when it's being built for display.

If you want to use the value on the node after update, use a hook like


hook_node_presave or
hook_node_update


instead.

To tweak your code snippet, something like:

/**
 * Implements hook_node_presave
 */
function mymodule_node_presave($node){
  if ($items = field_get_items('node', $node, 'field_vacature_scheduled_for_unp')) {
    $vacature = reset($items); // Use first field item value
    $expirydate = date("F j Y", $vacature['value']);
    $items = field_get_items('node', $node, 'field_unpublish_date')
    $unpublish = reset($items); // Use first field value
    if ($unpublish['value'] &lt; time()) {
      drupal_set_message(t("This vacature has expired."), 'status', FALSE);
    }
    else{
      drupal_set_message(t("This vacature will expire at: "). $expirydate, 'status', FALSE);
    }
  }
}