A webmaster posted in the Google Webmaster Help forums after noticing that one of his sites saw hundreds of pages wiped out of the Google index a week or so ago. He noticed that Google is associated one URL to a completely irrelevant canonical URL and suspects that is the issue.
The specific error he is seeing from Google Search Console is “Duplicate, submitted URL not selected as canonical.” He said “The problem is that the two pages are not duplicates and google selected canonical does not match the user selected canonical.”
Google’s John Mueller came in on Christmas eve and responded:
Usually this happens when we run across a number of URL patterns on a site that all lead to substantially the same content. If this all happened during a short time, it might be that there was something misconfigured that caused this, and in that case, it’ll settle back down over time as our algorithms confirm that these URLs are actually separate. That said, I agree that this looks really confusing, so I also forwarded these to the team to check out, in case there’s something on our side which we can do to speed things up for you :).
Here is one example of this site from the Google URL Inspection Tool:
Have you seen these types of errors before and it not be a misconfiguration by the webmaster?
Forum discussion at Google Webmaster Help.