Shoulder joint pain is not a known side effect from fish oils. The Tufts-New England Medical Center Evidence-based Practice Center (EPC) looked at 148 studies where fish oils were used. They found more than half of the studies showed no side effects from fish oils. Any reported side effects were mild; the most common being gastrointestinal in nature (diarrhea). Here is more detailed information on fish oil side effects. If your shoulder pain continues, I would recommend consulting with your health care provider or family physician to get further care.