Shoulder pain is typical after you receive a vaccine. That being said, the pain should be fairly well localized. It may be associated with some redness and swelling which can be treated with Acetaminophen, cold packs, and light massage. When vaccine administration is performed correctly this is a self-limited problem with minimal concern.
When vaccine administration is incorrectly performed to the sub-deltoid bursa, the inflammatory response can be severe with significant limitation in motion following administration. This can last weeks or months. Consultation with an orthopedic medicine specialist is often required. SIRVA can be associated with swelling and inflammation of the sub-deltoid bursa visible on imaging.
Treatment usually includes a steroid injection to the bursa and physical therapy. In rare cases a bursectomy (surgical removal of the bursa) is needed.
To be sure that you will not experience this, your vaccine should be administered by an experienced clinician that is aware of surface landmarks. The vaccine should enter the Deltoid muscle. The mistake of injecting the bursa occurs when the injection is performed deep to the muscle and usually more proximal (closer to the acromion) than it should be given. Patients can advocate for themselves by being aware of these surface landmarks.
Thomas S. Bottiglieri, D.O. 
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