A pull requests marries the entire branch to the one you're targeting; if you keep making changes here and there, a pull request will include all these new changes, regardless of when you originally opened it. It makes your request basically un-mergeable by upstream repositories, in most cases.
So the real procedure is:
- Fork the upstream repository. Now you have your own master branch. Clone it locally as usual.
- Create a new branch, either via web or (easier) from the command line with git branch FixBugBranch && git checkout -b FixBugBranch.
- Make your changes on this FixBugBranch. Make only the minimum amount of changes necessary to fix a specific issue, then commit and push.
- On GitHub, create a pull request from FixBugBranch towards the original repository
- When/if your pull request is accepted upstream, you can delete FixBugBranch.
If you want to make further changes, you can either create a further branch from FixBugBranch, or create and merge a pull request from FixBugBranch into your master. The important thing is that you don't touch FixBugBranch anymore, so that upstream maintainers won't receive all your extra commits but only ones relevant to the particular bug you raised.