This is just a list of strangeness that the github api has. These may or may not be actual bugs.
You can follow a user with the api, but you can’t unfollow them.
If you untick the bug tracker checkbox, the issues api still works and allows you to add issues as if the tracker was still visible on the github site.
You can view them on your project, you can see labels on their project you are a collaborator on in the web interface, but you can’t view those same labels in the api interface.