A lot of red delicous apples have whitish areas/stains on the outside skin. It is difficult to remove them even when trying to rub them off under running water. They seem to peel off when scratching with a finger nail. These white areas are barely visible but I would like to know what they are. Are they traces of pesticides?
Wax. It's why they can be so marvelously shiny if you buff them.
Pastorio
Usually carnauba wax, which is edible. Whether the surfactants they use to make the wax water soluble (and supposedly allow it to wash off easily) are I'm not sure.
Since the apple season is relatively short, growers or wholesalers need a way to keep the fruit from becoming dehydrated during long storage. Some large supermarket chains can afford to have special storage areas where proper humidity is maintained, but many don't bother. Wax is the answer. Put a drop of dish soap on a fingernail brush, splash some water on the brush, scrub, and then rinse the apples until they're squeaky.
If you live in apple growing country and spot an orchard whose retail outlet is open all year, try their apples. Some of these places have the proper refrigeration rooms, and can get away with using a wax that's much easier to remove.
I'm not sure what you mean by "stains," but Red Delicious apples normally have white spots on them. Does this photo look like what you're seeing:
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