Ollie is correct that any unusual pain deserves the attention of a doctor.
Your problem reminds me of the joke about the college student and the trainer. The college student demonstrated a move and said, "It hurts when I do this." The trainer thought about it and said, "Then don't do that."
You want to avoid all pain except fatigue on your long runs. These runs are often called "LSD" to emphasize the long, slow distance. Are you overemphasizing the "long" or underemphasizing the "slow?" If so, then try to cut your distance or pace. Experiment with various combinations of distance and pace until you find the one that allows you to go your desired distance without the weird pains(remember, the primary purpose of the long run is to build endurance, not speed).
Viola! With knowledge of an acceptable distance and pace for your long run, you can begin to increase the run's distance gradually.
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