This sounds very much like a surface pyoderma or bacterial skin infection.
It may be secondary to an allergy, probably an inhaled allergen as food allergies tend to cause facial, feet and ear itchiness.
I would have looked for demodex mites, and less likely, sarcoptes mites too. Both can lead to the type of lesions you are seeing by disrupting normal skin health and making her itchy. But if scrapings were negative there are other possibilities.
Certainly flea allergy could cause these types of lesions too, and so could a surface skin mite called Cheyletiella. We don't pick Cheyletiella up with skin scrapings as they live right on the surface of the skin and we find them by looking at a sample of surface dander under the microscope.
The other possibility is ringworm, so a fungal culture would be nice.
If she isn't on any type of flea and tick control she should be this time of year. Frontline Plus, Advantix or the new Seresto flea and tick collar are excellent. Don't use over the counter products, especially Hartz or Sargents, as most are ineffective if not toxic.
I would recommend placing an Elizabethan collar to prevent licking the area so she cannot further traumatize her skin.
You can also shave the involved area if there is a lot of hair in the area as that will allow it to dry out better.
In case this is an allergy related skin problem to relieve the itchy skin you can give:
1)Benadryl (diphenhydramine only don't use the combination products with acetaminophen or decongestants as they can be toxic to dogs) at 1mg to 2mg per pound of body weight or one 25mg capsule per 15-25 pounds of dog orally every 8 hours.
OR 2)Claritin (loratidine) at 5mg per 25 pound dog once or twice daily.
OR 3)Hydroxyzine at 1mg per pound orally every 8 hours.
OR 4) Chlorpheniramine at 4mg to 8mg per dog once or twice daily.
OR 5) Zyrtec (Cetirizine hydrochloride) at 1/2 mg per pound of body weight orally every 24 hours. That would be one 10mg tablet per 20 pounds of body weight. Make sure it is NOT the formulation with a decongestant (such as Zyrtec-D) because dogs cannot tolerate decongestants.
Some dogs do better on one antihistamine rather than another. You'll have to see which one works. Give whichever one you pick a week to 10 day trial and if it isn't working try another. Be aware antihistamines can cause sleepiness or hyperactivity in some dogs. These side effects do wear off with repeated use.
Omega-3 fatty acids are fish oil products. 3V by DVM or Derm Caps ES are good brand name products. I recommend a dose based upon the EPA portion (eicosapentanoic acid) of the supplement as if we do that the rest of the supplement will be properly balanced. Give her 20mg of EPA per pound of body weight per day. For example a 10 pound dog could take 200mg of EPA per day.
She should be bathed with an antibacterial shampoo a couple times a week. I like chlorhexidene shampoo, but Duoxo seborrhea shampoo can be very helpful for dogs that have a lot of scaly debris. Follow up with a conditioner, either Humilac spray (6-7 capfuls mixed with tepid water as a final leave on rinse) or Duoxo seborrhea microemulsion spray.
If she is no better in a week or so then she really should be rechecked by her veterinarian for an examination, some diagnostic testing and probably some oral antibiotics.
Please let me know if you have any further questions.