Toby has brown patches on the top of his mouth also. When I took him to the vet for a check up I asked her about it and she said that it was perfectly normal for a dog to have dark spots in their mouths. She said it is seen more commonly in pure breds than not. So, it's nothing to worry about. Being a first time mom of a furbaby I really worry about the smallest things so he is constantly at the vet!