HotCat stores part of its configuration on various MediaWiki pages which do not have a .js extension: MediaWiki:Gadget-HotCat.js/<languagecode> for localisations (such as MediaWiki:Gadget-HotCat.js/mwl; the page could be either on Commons or the local wiki) and MediaWiki:Gadget-HotCat.js/local_defaults on the wiki where it's used for configuration settings (such as MediaWiki:Gadget-HotCat.js/local_defaults). These pages are not recognizable to MediaWiki as Javascript; they should either be renamed to .js; protected from editing without the editsitejs right by some other means (e.g. GetUserRights hook); or (preferably) convert those pages to JSON and rename them to .json so that more people are able to edit it without being able to deploy sitewide JS. (That last one does not work for hook callbacks, but no WMF wiki actually seems to use them.)
HotCat is used on several non-WMF wikis, often by loading the main file from Commons, so care should be taken not to break those.