I don't think the problem is only because the whatsapp. I think that the iPhone doesn't show all data store in it.
When i plug my wife's phone to my Mac by a lightning cable and open iTunes i can see all data stored in iPhone but this is not the same information that the data and storage in settings shows.
I can see 30 songs as they were disabled, in grey color, and i can't delete them. I disable the icloud music library in the iPhone and try to sync with itunes but the set of songs still there.
If I turn on icloud music library again then thumbnails of albums, artists and other information is downloaded to the phone but they aren't showed in data and storage tab.
With icloud photo library enabled you can see how large is your photo library in the iphone, with thumbnails and albums, but this don't work in the same way with icloud music lib becouse you can't see how much data related to this is stored in your iphone.
I think apple might to do something to control the maximum data reserved to this stuff, music and photos.