im not exactly sure what ur talking about but....
on mine, i had some pretty bad sap stains on my hood, about 10 or 12, from the previous owner. So i clay bared it and then did the threee step, and yea, it made the sap stains stick out pretty bad, like little white dots all over the hood, it jus because the wax gets in there and dries leaving white residue. if u have a semi deep scratch or somthing that at least gets down in the clear coat, it will leave happy little wax residu for you to see. jus a cloth to a nice point and rub, pretty hard, to get it out, or maybe water, i cant remember.
if its jus on the paint in like sheets, and u can rub it off with a towel, just wax u forgot to polish off.
hope this helps..