Disqus injects code inside your webpage code. Consequently, it can trigger all sorts of SEO issues.
4xx errors
We checked the console of chrome on a website and we discovered there were 400 HTTP errors. We looked for the origin of the error. Since it was a WordPress installation we decided to uninstall the plugins. Guess what? We discovered that those 400 HTTP errors came from the Disqus plugin. After deactivating the plugin, the errors disappeared. Since the Disqus comment system needs to access resources, it can also create a 4xx HTTP error like a 404 HTTP error.
Google penalty
As I said before, since the Disqus plugin injects code inside your code, it can cause google penalties. For example, the Disqus developers may perform a change in the code that triggers a Google penalty on every single page where the Disqus code is available.
WordPress plugin issue
For WordPress installation, Disqus can be a threat just like any plugins because it has the ability to modify anything inside your code. This may not be limited to the bottom of your page. Disqus can add/modify/delete any code on the page. This is a safety problem related to WordPress. Every time WordPress loads a page, it first reads the code of every plugin.
Comment content
Then, we are always flip flop about the content of comments. All the google employees mentioned they want quality content. However, comments are not quality content. They are crawled and indexed but we don’t know if they can harm SEO or not.