Status message "The changes have been saved" displays when updating user data using AJAX and Services module
On your menu callback function ( at /api/internal/user/%user ) you can call drupal_get_messages('status');. This will clear the status messages displayed to the user. A better approach would be to check the message first:

$message = drupal_get_messages('status', false);
if( $message == t('The changes have been saved.') ) {
  drupal_get_messages('status');
}


If this is not a custom module, you should build one and use hook_page_alter() like this:

function yourmodule_page_alter(&amp;$page){
  if(arg(0) == 'api' &amp;&amp; arg(1) == 'internal' &amp;&amp; arg(2) == 'user') {
    $message = drupal_get_messages('status', false);
    if( $message == t('The changes have been saved.') ) {
      drupal_get_messages('status');
    }
  }
}