I always use "das" for Github issues and haven't heard the use of any other article for it.
Avoiding the word "issue" seems like a poor solution because this term is used a lot in IT and is specific to Github issues if the entire conversation is about a project on Github. "Issue" then doesn't refer to issues in general.
It very often is the case that the German article for the closest translation is used. "Issue" matches closely to "Problem" as well as to "Thema". Both of which are neutral. So it seems natural to go with "das" and that's exactly what's happening.
This does, however, not always work. Another example for common usage of English words in German IT context is "interface". The German translation is "Schnittstelle" which is female ("die"). The German article for "interface", however, is "das" (neutral). Maybe that's because "face" (Ger.: "Gesicht") is neutral. But sometimes the articles people go with don't make any sense whatsoever.