git not adding existing folder

A subfolder will not be added with git add . (or similar commands) if it contains a .git dir because it will be assumed to be a git submodule.

You can rm -rf .git in the subfolder if it's not supposed to be a submodule.

Are there files in the folder? Git doesn't track folders, only files; you can't add an empty folder to a Git repo. However, you can put an empty file in that folder (.gitignore or .blank are common file names) and add those files to the folder.