Can pokemon have different markings than the ones in “official artwork” or in the pokedex? For example are all Charmanders plain orange and cream, or could they have, say, a few brown spots or something?

If by “official artwork,” you mean photographs in the pokédex, absolutely. The pokédex images are merely photographs of the specimen a trainer or researcher has on hand. Actual wild pokémon may possess markings that might vary greatly due to a number of factors, including environment, certain genetic factors, physical condition, and so forth.

More specifically:

• Pokémon may change colors in response to their environment. This not only refers to adaptive evolution but also individual response to environmental influences, including the chemistry of the available food sources. For example, even visiting pokémon to Pinkan Island in the Orange Islands archipelago have been known to turn pink due to the fact that pinkan berries—a rare, pink berry that happens to be high in lycopene—are the most reliable food source for pokémon on the island. (On that note, it’s highly recommended that trainers feed their pokémon commercially produced kibble while on the island unless they want a pokémon the color of a jigglypuff.)
• But yes, evolution is also a possibility. Take the Alolan and Kantonian vulpix, for example. Vulpix in Kanto have adapted to warmer climates, and hence, they possess a fire-red coat of coarse, short hair. Alolan vulpix, meanwhile, thrive primarily in colder, snowier climates. Thus, they sport snow-white coats that allow them to blend in with their surroundings, and their fur is thick and soft enough to trap the heat they need to survive cold, wintry nights.
• While pokémon inherit the species of their mother (unless that mother is a ditto), it’s not at all unusual for some to inherit traits from either parent. It’s not normally so drastic as to produce pokémon that are entirely a different shape or color than the ones you might see in your pokédex, but as an example, a meowth whose father was a pikachu may have more golden fur than normal, whereas a meowth whose father was an eevee may have thicker fur around the neck and a bushier tail. In short, the meowth will still be immediately recognizable as a meowth, but certain traits may be slightly different from the official photograph thanks to its father.
• Pokémon fur, skin, and so forth are notably more vibrant the healthier the pokémon in question is, and likewise, fur will usually be thicker and shinier. By contrast, duller, grayer, or thinner fur or skin indicates a general illness. Likewise, pokémon with unusual spots, lumps, or moles may be suffering from cancer, cysts, or other unfortunate conditions, and pokémon can certainly be born with deformed limbs. Alternatively, some injuries sustained on the battlefield or elsewhere may lead to permanent damage, such as scars, missing eyes, torn limbs, and so on. Old age can also bring about arthritis, which in some pokémon pronounces itself via enflamed joints. If your pokémon suddenly changes in physical appearance or if you have a pokémon with any physical condition that seems a little unnatural, it’s best to take them to a pokémon center for an examination.
• Of course, these are just a few of the most likely possibilities for an explanation as to how you might acquire a pokémon with unusual spots. There are certainly others as well, including the possibility that you’ve just encountered a specimen in a particularly dire need of a bath.