Holes Drilled on Purpose
Tiny holes in shingles are sneaky because they can cause rot and other damage for years before you notice the obvious signs of a leak. You might find holes left over from satellite dish or antenna mounting brackets or just about anything.
And exposed, misplaced roofing nails should be pulled and the holes patched. Small holes are simple to fix, but the fix isn’t to inject caulk in the hole. You’ll fix this one with flashing.