Muscle atrophy. Anything that damages a nerve or the muscle(s) innervated can cause atrophy. There are many conditions that can cause this like a pinched nerve that might have been painful, then healed but left atrophy. There are disorders of motor nerves, as well as muscles themselves that cause atrophy. Central nervous system changes would likely lead to less severe atrophy, mostly from inability to use.
Many answers. Most important are: trauma; damage to nerve connected to the muscle(s) involved; genetic diseases of metabolism, nerves or muscle; excessive pressure on a muscle for a prolonged time (>3 hrs); poor circulation to a muscle; infection in the muscle itself; repeated corticosteroid injections into the muscle.