I just had this exact same problem, but AFTER it was working
It happened because I had to reset the gh-pages branch. So I
- git branch -D gh-pages
- git push -d origin gh-pages
Then I had a script create an orphan branch gh-pages, populate it, and push it. Before this, everything worked without /index.html, but after, I had to add /index.html. I must have triggered a bug by accident.
The fix was was go into the settings and change the GitHub Pages Source branch to master, then back to gh-pages. This toggle was able to get around the bugged state I found myself in and everything is good again.