There are two possible causes for this condition.
One is the increased anaerobic metabolism of local muscles and other tissues during pull-ups, where metabolic products such as lactic acid accumulate and so cause a feeling of soreness.
The second is that high intensity or incorrect pull-ups may lead to external damage to the bones, muscles, tendons and nerves around the shoulder joint, resulting in strain, inflammation and compression, leading to osteoarthritis, tendonitis, fasciitis and even fractures and dislocations causing pain.