Currently, the simplest way to resolve this situation is to pick one of the issues to be the main one (whether the best documented, oldest, or whatever). Then, add a comment to the other issues linking to the main issue and close the duplicates.
Here’s an example.
Here’s another showing the “Duplicate of #123” syntax.
Alternatively, you can leave the issues open and reference them all together in your commit messages: Example.
I imagine that in the future, the team behind GitHub will make this process easier.