I have met the same issue.
In my case, I have deployed a SNAPSHOT version of my simple project. And after updating the project, I’d like to deploy the snapshot version again but Maven returns an error with status code 400 just like this issue. In the other side, all thing works well with RELEASE version of my simple project.
I guess there is something wrong(maybe bugs) with SNAPSHOT in GitHub Package Registry.
PS: to recurrent this issue, just create a simple maven project with a snapshot version(such as 1.0-SNAPSHOT), deploy it to GitHub Package Registry, and then update it and deploy with 1.0-SNAPSHOT again. Hope this helpful.