In my experience, when you clone an asset and try to select a folder to place it in, it will only display top-level folders.
Subfolders that are located inside that top level folder do not appear in dropdown of available folders to place cloned asset. So you have to first clone to top level folder, then once it's been created go in and manually move it to the subfolder.
It would be nice if subfolders appeared in cloning location options.