I typically create a repo on Git to start, and then use the following to clone the repo:
git clone git clone [email protected]:username/name-of-repo

I do this from within my ~/GitHub directory, and when I look into the .git directory of my newly cloned repo it contains the directories of all my other repos, as if it has copied each one of them into this new repo too.

I have looked at the config files and it looks typical. I have tried deleting and redoing, but it does it each time.