I bought a kitten from the pet store last week. She has adjusted well and is a well behaved kitten. She was perfectly fine physically until last night, when she began walking with a limp in her left leg. I thought maybe she had broken her leg, but this morning when I let her out of her cage, her left leg was fine and she has now began to limp on her right leg. Could she have a physical disability that causes this to happen, or could it just be pulled muscles?

Yes, but it's called Cerebellar Hypoplasia in felines.

Only a vet will be able to tell you if your kitten has CH.