Brief Answer:
several ways to approach this.

Detailed Answer:
One I tend to use is to go from what is in the area that could hurt and go from there. The most common shoulder injury is ROTATOR CUFF.
http://www.hopkinsmedicine.org/orthopaedic-surgery/specialty-areas/sports-medicine/conditions-we-treat/rotator-cuff-tear.html?utm_source=eruptr&utm_medium=cpc&cr=ortho&utm_campaign=ortho_knee_surgery
Generally people know why they have the problem and it is generally on the OUTSIDE and TOP of the shoulder. It hurts to touch.

There can be a problem with muscles. These can be sore from use--acute or chronic. They can also be sore from pressure, trauma, laying on it wrong, or muscle disorders. They are sore with moving the muscle.

There can be an underlying problem with the lung. Pain with coughing and breathing would be an indication this is occurring.

There can be tumors, growths, lymph nodes or even infections and boils. These are generally pretty obvious.

That is pretty much all that is there.

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Brief Answer:
And related issues.

Detailed Answer:
It's a very common spot for deep infections (which have pain, swelling, warmth, purulent boils popping out) and lymph nodes. The skin/sweat glands can easily get infected and the folds of skin can be hard to get the infection out without (minor) surgery.

https://www.healthtap.com/user_questions/0000-i-have-lumps-that-appear-in-my-underarm-after-my-period-they-will-often-burs

heh, but why believe that guy !!!

http://www.mayoclinic.org/diseases-conditions/hidradenitis-suppurativa/basics/definition/con-0000

Key points would be the localization of the pain. With any inflammatory process it is One Spot. WIth nerve or muscle pain it is a broader area involved. Also, would expect signs of infection/inflammation like increased warmth, swelling, or redness....but it can be rather deep in.

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