Not sure how you installed them but just in case, the Numix team provides a PPA to have the latest version of the icons & themes (and also some that are not in the Ubuntu repos, like the square icons).
AFAIK, there are no variants of the folders with different colors like there used to be a few years ago IIRC (default one should be a light orange) though the theme supports Folder Color. But Folder Color doesn’t allow to set an alternative default color anymore.
Unless your folders use the yellow variant, which would be weird (can you post a screenshot to confirm this?), the only “easy” way I can think of to use a different color for the folders would be to create a custom theme with the one you want that depends on Numix and use it instead in the Appearance prefs.