GitHub keeps saying “This branch is X commits ahead, Y commits behind”

As you guessed, these extra commits are likely the merge commits from the Pull Requests that you created.

In the future, there’s a much easier way to sync your fork with the original repository. In your local repo, after the initial clone do:

git remote add upstream https://github.com/upstream/repo.git

Then, whenever you want to sync the changes from upstream, do:

git pull --rebase upstream master
git push --force-with-lease origin master

(The --rebase and --force-with-lease options will only be necessary if you have commits that haven’t been merged into the upstream repo.)

_{Obligatory warning: Since a rebase rewrites history, this can be dangerous / disruptive for anyone else working on this branch. Be sure you clearly communicate what you have done with anyone you are collaborating with. Since this is a personal fork, I assume this won’t be an issue for you.}

Now to fix your current issue after the fact.

1. Add the upstream remote as described above.

2. Reset your local branch to match upstream:

   git checkout master
   git reset --hard upstream/master
   

3. If you have created any commits in your fork, you can cherry-pick them onto your updated version of master. If you can’t remember or need help finding them, something like

   git log --oneline master origin/master
   

   should show you any commits not in upstream.

Above I assumed that you are only using one branch, master. If you aren’t already, I highly recommend that you create a new branch for each feature / bug fix that you work on. Among other benefits, this allows you to start work on another feature / bug fix when you are still waiting for an earlier PR to be merged. If you never commit directly to master, then you can sync without the --rebase or --force-with-lease:

git checkout master
git pull upstream master
git push origin master

To update a feature branch after you have updated master, do:

git checkout myfeature
git rebase master
git push --force-with-lease origin myfeature # if you have already pushed