To me that looks like GitHub (basically internally with Jekyll) rendering your index.md and not Franklin, as if the gh-pages/deploy from GitHub dies not take the __site folder but the markdown files from the main folder. Can you check which branch GitHub publishes?
So one settings → Pages should look something like this (from my Franklin page GitHub - kellertuer/kellertuer.github.io: My science profile page. Written in Franklin.jl)
