If a page is paginated: true, all pages (except the first) contain the paginate_path in the github_edit_link.

I created a minimal demo here, but if you have the following config:

repository: "owner/repo"
paginate_path: "page/:num/"

and an index.html with paginated: true, then when you visit /page/2/ the github_edit_link will contain /page/2/index.html instead of just /index.html.

The issue here would seem to come from jekyll-paginate, because the page.path is set to /page/2/index.html. It seemed better to raise the issue here since that repo is not maintained.