I'm not sure about other toy breeds but majority of these little ones seem to be sensitive to food. Just going by your description, sounds like allergy but I could be wrong. It's best to feed them food that is grain free and if you can afford it, both grain free & holestic food. (This is my own personal opinion.
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The allregy also could be environmental. Personally, I'd change to a different food first and try to eliminate other possible sources one at a time. Could be some detergent, perfume, etc..
If ever in doubt her health, go to the vet. Magnus had similar issues couple years back. I took him to the vet and she said he had a mild skin infection from all the rubbing/scratching. Turned out to be allergies so whenever I see him rubbing/scratching his face, I give him benadryl.
I hope she gets better soon!