I had this exact same problem. I received my flu shot at our local Walgreens on Oct. 1st. When she gave me the shot, I thought she was giving it to me higher up on the shoulder than normal, but I didn't say anything- thinking she knows what she's doing. After having shoulder pain for about 6 weeks, I went to my family doctor- he said it was possible the injection was given in my bursa sac. He gave me a prescription for pain relief- and within 2 weeks, the pain was gone. Everyone else thought I was crazy- the pain had to have been from something else- but fortunately I have a family doctor who was very helpful!