This template adds the following categories to Citoid, but is Citoid a skin?
Topic on Template talk:Used by
It's because Module:Used by assumes that anything that isn't an extension is a skin; see the if statement starting on Module:Used by#L-18. This should probably be fixed, but I don't know if that would require changing the format of Module:Used by/data.json as well (which would *also* mean changing the tool(s) used to generate the JSON, and potentially notifying somehow for any reusers of the JSON data, if there are any).
It seems to me that the real problem here is that the page Citoid covers both Citoid the Node.js app, and Citoid the MediaWiki extension that wraps around it. Is there any objection to moving the extension-related stuff to the page Extension:Citoid?
Okay, I decided to "be bold" and make the move. Everything looks fine now, I think, assuming my changes don't get reverted.