A file that is embedded in a post, will not show up in the usage section of the file page.

e.g. the image embedded in the first post here, https://www.mediawiki.org/wiki/Topic:Sfbyjm0fpw0kkb9k
is not listed in the https://www.mediawiki.org/wiki/File:Unprintable_chars_now_visible.png#filelinks section
(but the direct [[:File:...]] link to it, in the post below, is listed there.)
However both the embedded version and the linked version, are listed at https://www.mediawiki.org/wiki/Special:WhatLinksHere/File:Unprintable_chars_now_visible.png

See also:

• T59512: Flow not storing database link tables (pagelinks, categorylinks, imagelinks, etc.)
• T67671: Flow: "File usage" on Flow boards doesn't link to topic
• T70343: Flow: links in Flow posts don't update SpecialWhatLinksHere
• T67878: Flow references in "File usage" section of a File: page don't have post/header links
• T92571: Have WhatLinksHere show full information for Flow content
• T69398: Flow: Special:WhatLinksHere is not differentiating links from transclusions
• T96810: Apparent lag in picking up links (to file pages)