Atopy" is a skin disease and nearly 30 percent of dogs suffer from it. It is allergic in type. Your dog is suffering from it if it plays in mud. This can be cured by antibiotic medicines. Get your dog to vet for checked up. Take some anti-viral shampoo and give bath to your dog. It will remove black spots from its skin.

You are right; it can be a sign of bad food as well. This disease refers to "Food Allergy" that causes bump in pets, especially in dogs.