Since Disqus is made for static site comment system, each Disqus thread is identified by the current page URL. This leads to a problem that Disqus does not understand that http://my-site/link/to/post and http://my-site/link/to/post/?fbxxx refer to the same article. The second link is caused by facebook sharing system. It automatically add the trailing to the links that shared on facebook. As a result, those 2 links are considered as 2 separate threads and will not display probably.
The solution for this is to normalize the URL of the site to make them all follow one convention. Because Jekyll sites are static websites, we need a language that can run on client. This can be solved by using javascript.
Inside the _includes folder under the root directory of your website, create a new file named normalize_address.html with this content
The code above handles the URL, removes the unnecessary part in the URL and redirects viewers to the new normalized URL. Next, we need to include it into our layout so that it is auto-loaded everytime the guests view the page. Open the file default.html in _includes/themes/your-current-theme/ (your-current-theme is the name of your current using theme). Add this to the header of the page