https://houkai2nd.miraheze.org/wiki/Special:UnusedFiles
For example this particular Nyarlathotep icon file is used in infobox but file usage listed as none
https://houkai2nd.miraheze.org/wiki/Nyarlathotep
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Special:WantedFiles does not pick up images used in infoboxes, for that they would need to be used elsewhere using mediawiki format for files. There is no way that I am aware of to make it pick up from infoboxes. I apologise for the inconvenience.
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Definitely not infobox bug, checked another file that got the same issue
https://houkai2nd.miraheze.org/wiki/File:Infinite_ammo_during_combat.png
https://houkai2nd.miraheze.org/wiki/Category:Infinite_ammo
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I maintain the PortableInfobox extension. I am 100% aware that the images set there do appear on Special:WantedFiles. It's been a long-reported and known issue with the extension, and I'm unable to fix it. https://houkai2nd.miraheze.org/wiki/File:Infinite_ammo_during_combat.png is not used on any pages either, that I can see, and no images are used in some pages on the category, so not sure what your linking to there?
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This is UnusedFiles, not WantedFiles.
The file https://houkai2nd.miraheze.org/wiki/File:Infinite_ammo_during_combat.png is used in https://houkai2nd.miraheze.org/wiki/Category:Infinite_ammo but was listed as unused which is kind of weird.
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I checked around and noticed that pages that never got edited after imported (or after updated MW) seems to have this kind of issue.
Edit: Alright, I can fix the issue myself since there are very few pages needs to be fixed.
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Please give it until the 25th, which is 10 days after the upgrade, which is what our parser cache expiration is set to. Based on the fact null-editing fixes the issue, I'm assuming it's in relation to Parser cache. I could be wrong, but after the 26th if the issue still persists, please provide another non-infobox example. Thank you! I apologise for confusion and inconvenience here.