When researching to see if there has ever been an animal featured that isn't a Pokémon in a scene or Manga I came across this on Bulbapedia's article Animals in the Pokémon world:
Real-world animals have been mentioned a number of times to exist in the world of Pokémon. Most often, they are mentioned in relation to a Pokémon category. For example, Pikachu is known as the "Mouse Pokémon" and was directly referred to in the anime as an "electric mouse", hinting that real-world mice exist in the Pokémon world. Other than this, all other mentions of animals are rare.
There was also this image:
Which clearly shows a dog. However, this is the only image I could find of an animal that isn't a Pokémon.