We have seen brand new roofs with this very same defect.  You expect the
job was completed professionally and to your satisfaction, but did you
actually  go up there and inspect the work?  Most of us don't because we trust
the contractor, and by the time we see that new roof, everything looks
wonderful.  
A small opening like this one can, over time, cause extensive deterioration to
everything from sheeting to insulation, all the way to your walls and the paint
on them.  The damage inside the walls and the ceiling is hidden, and may be
festering for a long time before you see an active leak.  
Moisture, again, causes rot and may attract carpenter ants, leading to further
problems.
Early repairs will be minimal, waiting could be costly.


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