Whenever an object like a chimney or plumbing vent pipe protrudes through a roof surface, there must be protection / flashing installed around the item to prevent water from running down around the item into the attic or living area below. In the photo below someone ran a plumbing vent pipe up through the roof surface and simply folded up one of the roof shingles. This was not likely done by a professional roofer and water leakage at this roof opening is a certainty.

Photo taken by Phillip Stojanik of Pro Check Inspection Services, Houston, Texas.