This is a rabbit hole to go down, given there are so many opportunities go off the rails when it comes to the kipping pull-up. In PT, I honestly see or hear about this often. While every case is unique, there are a few common themes you seen when an athlete has shoulder pain with the kipping pull-up.
In general, I would say most shoulder problems with the kipping pull-up are rooted in at least one, if not multiples from the following list.
Incomplete/missing overhead mobility
Not creating an active shoulder under the bar (Yes, skill and strength both play a part in this)
Not doing #2 well when you are fatigued
How well do you stack-up as an athlete? Get started by checking your overhead archetype and doing something about it if you are lacking. (Video Link)
More to come in the following weeks! Stay tuned.