I'm not familiar with Github hosting, I've just used Github for commenting on issues and an occasional pull request. Is this some built-in interface that requests certificates on your behalf and that error is all that you see? If so, I think it has to be something on their side.
The only current issue is with the test certificate transparency system (Testflume). Other than that, the last issue was a couple days ago. Actual normal certificate issuance should be working fine.
It's possible that they're checking the status API but not actually checking which Let's Encrypt service is down. The Testflume outage has been happening for a month now and I don't see any indication of when it might be back up, so if that's what's stopping them they need to work on fixing their system to only look at the status of the certificate issuance and not the test Let's Encrypt services. That's all just a semi-educated guess as to what's happening, though.