After you submitted your assignment and received your feedback, chances are it was closed without being merged into the remote master (the official course repository). You now have a fork that is not in the same state as the official copy and you need to sync it back for the next assignment. If you don't, future pull requests will include the previous assignments and will create a mess.
There are two main ways to get back to sync and one way to avoid this problem in the future:
This is the simplest. You just go to your fork on GitHub, go to settings and at the bottom click on Delete this repository. Once deleted, go back to the official repository and fork it again. All set. Remember to also delete your local directory and then to clone your new fork all over again.
git remote add upstream https://github.com/hueniverse/hueniversity
git fetch upstream
git branch backup
git checkout upstream/master -B master
git push origin master --force
You are now back in sync and can start the next assignment
Once your fork is in sync (using one of the two methods above), do not make changes directly to your master branch. Instead, make a local branch for the current assignment:
git branch assignment1
git checkout assignment1
Make your changes as instructed by the assignment and save them.
git add .
git commit -m 'my changes'
git push origin assignment1
When done, go to your fork on GitHub, switch to the assignment branch using the button on the top left, right above the file list, and then initiate a pull request.