Steps to recreate:

1. Create a fork of a GitHub repo (in this example, originalRepo). Do not create a GitHub Branch Source multibranch project for this yet.
2. In this new fork, make changes in your master branch. (Actually, any branch will probably do, I just picked master)
3. Push the change to your newly-created fork.
4. Create a PR from your fork/master, to the original repo/master.

5. Now, create your multibranch project for originalRepo. Make sure that the Discover Branches strategy is set to the default of Only branches that are not also filed as PRs.

6. Examine the Scan Repository log. You'll see something like this:

Examining cloudbees/quality-assurance
  Checking branches...
  Getting remote branches...
    Checking branch master
  Getting remote pull requests...

Notice that there's no Met Criteria or Does not Meet Criteria message. This is a tell.

7. Go back to the top of your project for originalRepo. There's no master branch shown.

8. In GitHub, merge (or merge/close) the PR.
9. Rescan.
10. The master branch will appear.