One folder is missing in git and pushed as a file

That icon, and the hash ID next to it, imply that what you have is not a file at all. (And, Git doesn't store folders, so it's not a folder either.) What it is, is what Git calls a gitlink. A gitlink is the internal piece of a submodule that tells the superproject which commit to get out of the submodule.

A submodule is itself just another Git repository. That means that after cloning the superproject, you must git clone the submodule repository as well. The instructions that let Git do this on its own are stored in a committed file named .gitmodules. If the .gitmodules file is missing—as appears to be the case from your screenshots, if they're complete—then Git itself can't git clone the submodule for you. I like to call this a broken submodule, or sometimes a half-assed submodule. To fix it, you must supply the other half of the ass: clone the appropriate Git repository. (Then put the instructions into a .gitmodules file, too, so that it's fully-assed next time.)

If you don't want a submodule, don't use a gitlink. To make Git not use a gitlink, make sure that you're not trying to add a repository to a repository: Git literally can't do that, so it makes a gitlink instead.