I'm not sure if this will be much help, but did grab a couple screenshots in hopes that it'll help.
(Click images to see larger view)
Your Sims 4 Folder should look something like this:
And your Mods folder - new - nothing in it but the resource.cfg should look like this:
What may have happened is that the user files from the Sims 4 folder got copied into the Mods folder by accident.