Diagnosing stress fractures isn't easy. As you know they don't show up on X-rays in the early stages. This is called a false negative. In other words, the X-ray was read as normal when there really was a problem.
Bone scans have the opposite problem. They often indicate there is a problem when there isn't one. This is called a false positive. False positives are more common with children and teenagers who are still growing or remodeling bone.
MRIs seem to offer the best results when looking for bone stress injuries. In a recent study of military trainees with exercise-induced knee pain, two separate radiologists read the patients' MRIs. They did this without knowing the patient's symptoms or history. They didn't consult with each other. There was good agreement between the two physicians and an accurate result with the MRI.
MRIs can't show the difference between bone bruises and bone stress injuries because bone marrow edema is present in both. In such cases the physician must rely on the history.