When an old roof was removed some of the “H-Clips” were bent upward and the previously used roofing company did not make sure that all of the “H-Clips” were flat before installing the new roof. This caused the metal clips to pierce through the new roof, creating a leak from a roof that was only about two years old. This is what happens when storm chasing companies are more concerned about volume rather than quality work. They pride themselves on doing a roof in one day, but that comes with consequences.
If you can find a needle in the haystack and pinpoint the cut, either seal the area or remove the shingle & install a new one. It can be challenging to see it sometimes.