I created a template called Template:Switzerland-river-stub and immediately saved a page with this template. The template showed up as a red link (even though the page of the template was loaded before I started saving my edit to the article). Null edits didn't help; however, a purge for the cache did help.
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This is probably just a delay with the JobQueue. Was it on a WMF project or a personal MediaWiki install?
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It was on English Wikipedia. I thought, though, that the job queue applies only for edits to the template saved after edits to the transclusing page; here I waited until the template was saved before saving the article.
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I don't really see a bug here apart from "JobQueue was large"... hence closing as invalid because things worked 'as usual' (just with delay).