Your experience with the influenza vaccination is an unfortunate and infrequent occurrence.
An improper injection into or around the shoulder joint can result in an inflammatory response (for example, bursitis). Also, if the injection is given "too deeply" -- at the surface of the upper arm bone (the humerus), there can be inflammation of the bone as well. This is quite rare but possible depending on the technique of the vaccine administrator and the anatomy of the person receiving the vaccine.
In addition to soft tissue, muscle, and periosteal (around the bone) inflammation, nerves can be irritated or even traumatized by a vaccination. Or, an inflamed bursa can cause referred pain that may extend down the upper part of the arm.
I would encourage you to remain as active as you can and to use your shoulder and arm as much as you can tolerate. Ice therapy applied to the areas where you have discomfort can provide significant relief. Physical therapy may provide relief.
Your symptoms should become less and less over time. However, the complete recovery may take weeks to months.
I hope that this comment/answer is helpful to you.
Also, here is a previous posting and answer that you may find helpful.
~•~ Dr. Parks
This answer is not intended as and does not substitute for medical advice. The information presented in this posting is for patients’ education only. As always, I encourage you to see your personal physician for further evaluation of your individual case.