Yes! This may not be an immediate issue but it could lead to leaks and other roofing problems over time. The primary reason for this could be the incorrect screw placement. Screws should never be so near an open edge or a path of water.

The shingles around the chimney flashing need to be replaced. And the penetration should be secured at least at a distance of 6” from the edge flashing on the new shingles.

This will avoid the problem in the future.