Disqus has always been a challenged for Google but several months ago, they made their commenting rendering engine more search engine friendly - but many were not convinced.
That being said, recently, several bloggers noticed an unusual spike in 404 errors reported by Google Webmaster Tools. They dug into the issue and it seemed like it was coming from the Disqus commenting engine.
Here is a picture of the weird 404 errors that make no real logical sense (it should show URLs, not numbers):
Google's John Mueller said he'd look into it but in the meantime, the webmaster emailed Disqus support who blamed Google. They wrote:
So hopefully, the two of them will be able to fix the issue.
I have seen an unusual spike in complaints about these errors in the past week or so.
Forum discussion at Google Webmaster Help.