I don't think anyone has any ideas for you.
I have no idea. I guess it could be allergies/rash. If Ellie had them and they didn't go away in about 3-5 days or she kept getting more, I would talk to the vet.
Those two foods are not really good at all though. I used to feed Pedigree canned and Science Diet kibble and regret it now. There are lots of threads here about good dog food that you can search for in the Health and Diet section. I personally prefer homecooking.