John Mueller of Google said on Twitter that Google will count the same URL in different sitemap files separately, which could sometimes lead to the number of URLs in your sitemaps being less than the number of URLs counted as being indexed.
An SEO shared a sitemap report showing this:
Here are the tweets:
The same URL in multiple sitemaps is counted separately, which is why you could see something like that. I'd keep URLs in a single sitemap.
— John ☆.o(≧▽≦)o.☆ (@JohnMu) August 16, 2017
Is this the only reason the number of indexed URLs would be higher than the number of submitted URLs in the sitemap report?
Forum discussion at Twitter.
