I was replicating this on my local server and it works fine so it’s not from the plugin or theme, the variation that is out of stock doesn’t show in the quickview or in the product page.
This somehow seems some plugin conflict or cache issue, if you select a variation in the quickview modal you can see that after that he size 13 goes away.
https://www.dropbox.com/s/zdk98rzr2q819vq/Screenshot%202017-01-18%2015.43.01.png?dl=0
Try to disable all the cache mechanisms and disable all plugins except SwiftFramework, Woocommerce and Woocommerce Quickview.
-Rui