I think where you have made your mistake is not to include All the categories and subcategories in the new product/product update section.
I've attached 2 screen shots from the categories section of my site that illustrate what I'm talking about.
Also when you add a new product that will have options you need to make sure to update all options that will be the same throughout that product and it's variations.
In my case I would not choose to "update all options" as regards quantity available for example.
Looking at your site I would venture to say that "Hawk Brake Pads: Genesis Coupe Brembo Brakes" does not include "Hyundai" or "Genesis Coupe 2.0t" as categories in the product update section.