Many times during the new construction process roofing crews will use toe boards as a means of safety and stability on steep roofs when installing the shingles. This is a common practice along with other means of safety such as roof jacks and harnesses. However, many times the roofing crew will get in a hurry upon completion for the day or simply forget one very important item before getting off of the roof. The nails that hold the 2 x 4 boards and serve as toe boards leave holes when removed. The nail holes, when left un-caulked, become weeping leaks that will never been known until the homeowner is in the attic many years later or when it is finally time to re-roof the home.
This is not something that only pertains to new construction roofing crews. Over the years of owning a home, or as the home is bought and sold, there may be repairs done. The repair crew may also use a toe board for stability and safety. If the same mistake is made and the nail holes are not caulked, the same type leak will occur over time.
The bottom line, make sure to check the roofing deck from the attic annually if at all possible and more importantly, hire local and certified professionals that you can trust to take care of every detail when working on your home.