There is a small update to the theme. Thanks to Mathew Turland for pointing it out.
In theme.php the line
$this->assign('nav_pages', Posts::get( array( 'content_type' => 'page', 'nolimit' => 1 ) ) );
was changed to
$this->assign('nav_pages', Posts::get( array( 'content_type' => 'page', 'status' => 'published', 'nolimit' => 1 ) ) );
to prevent deleted pages from showing up. You can download the new theme now or just replace that line in theme.php.