To be disfigured is to be misshapen, awkward, and otherwise unseemly in appearance compared to what would be perceived as normal (with caveats about "what is normal?" applying.) Something may be considered disfigured if it has things missing, if it has too much of one thing, or if one thing is highly irregular in shape or size.
Perhaps the most famous case of disfiguration is that of Joseph Merrick aka The Elephant Man. Born with an outrageous case of Proteus Syndrome, many parts of his body grew to large and grotesque proportions. Despite his disability, Merrick lived what could admirably be called a normal life. My mother, who suffers from polio, has one leg significantly shorter than the other; she, too, would be considered "disfigured", though you wouldn't know it by the way she gets around the house.
In art, things that are disfigured or distorted are often done so with a technical and symbolic eye. Salvador Dali and Pablo Picasso are famous for their use of out of place configurations to explain their thoughts on death, sex, and art itself.