Nanook has those & it used to be worse, especially when he would dig a lot. Although he had no problems, no itching, shaking, whining, etc... because it was mostly just dirt. It took a little bit of work getting it clean again. I'd put a warm moist cloth on it for a while, repeaated until it was easier to scrub off. And I honestly think some of them on Nanook are freckles because there are some that NEVER come off.

Because Josie is shaking her head and holding it weird she may have something else going on, either a little dirt, a possible infection starting, even a loose piece of hair or grass in there.

I would suggest you try cleaning the spots like I stated above. Then to help with the actual ear problem I would clean her ears well with a ear wash/drying solution. I'd wait a day, and if she is not acting any better I'd repeat the ear cleaning and then add a little of the meds from her last ear infection (ONLY if it has not expired) for another day or 2. If she doesn't improve then I'd get her to the vet, if she worsens then I;d stop what your doing & get her to the vets.

Do the ears smell bad?

Ear mites look like coffee grounds IN the ear canal, they usually don't hang around on the flap unless it's a major infestation.

I don't think it's anything too serious as you said the ears are not red at all.

Good luck.