Meta data is output twice

WordPress version: 3.5.1
WordPress SEO version: 1.3.4.4

For me, the plugin outputs the meta data twice. It happens on all install I’m using Yoast SEO on. Here’s a screenshot of what I mean: http://cl.ly/image/3L2T3e29122J

It happens for everything i fill out. Ie. if I fill out Facebook Open graph meta data it’s output twice.

You can look at my source code for reference here: http://ahrengot.com/

And here’s the PHP I use to generate the head section. Notice I’m creating the Open Graph data manually to circumvent this:
https://github.com/Ahrengot/Ahrengot-WP-Theme/blob/master/head.php

I really can’t figure out any logical reason why this is happening. I’m very grateful for any feedbacks or ideas to fix this.

http://wordpress.org/extend/plugins/wordpress-seo/