Thanks for a clear bug report. Much appreciated!
I can't duplicate the problem with the systems currently available to me. I've created a test job which uses `milestone` and `checkout scm` as described in the bug report and have run it successfully in several different multibranch Pipelines on my test server.
I don't have convenient access to install the Disable GitHub Multibranch Status plugin on that test server. The hotel where I'm staying on business travel blocks my ssh access to my test servers at home.
Could you attempt to run your failing Declarative Pipeline on a server which does not have the 'Disable GitHub Multibranch Status' plugin installed?
I won't be able to explore this further for at least another two weeks due to business and personal travel.
In the interest of full disclosure, I ran my tests on the latest released versions of all the workflow plugins and the latest pre-release of the git plugin and git client plugin. The specific plugin binaries I used are on the lts-with-plugins branch of my docker-lfs repository.