See the screenshot below. I'm not sure how to troubleshoot or replicate this issue. If someone gives me direction, I may be able to provide more info. I just stumbled upon a file page where the "What links here" did not match the "File usage" and I would expect them to match.
"File usage" only lists pages that embed the file directly on-page ([[File:Example.png]]); "What links here" also lists all pages that link to the file's description page ([[:File:Example.png]]). I've always thought the messaging in the "File usage" section was misleading.
You can modify the message via MediaWiki:Linkstoimage (for files that are used on at least one page) and MediaWiki:Nolinkstoimage (for files that are unused). I've modified both of these on a couple of the wikis I am/was an administrator on, see examples on Yugipedia: MediaWiki:Linkstoimage, MediaWiki:Nolinkstoimage.