I see this message when trying to enforce https on my github pages website with a custom domain, which I registered through GoDaddy. The message showed up when I first linked my custom domain, but it's still there a week later.
Other Context:
What might be preventing the certificate from going through?
I found the solution here. The problem was that I hadn't deleted the A record that GoDaddy automatically includes, parking your website. I deleted this A record and the certificate went through within a few minutes.
This question describes a different problem with the same solution.
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