What is the weakest part of a roof?
Anywhere the roof surface is broken up. Leaks rarely start in the middle of a plain field of shingles.
The usual weak spots: metal flashing around chimneys, skylights and walls; valleys, where two slopes meet and funnel water together; rubber boots around vent pipes, which crack after years of sun; and the eaves, where ice can dam meltwater back under the shingles.
These are repair jobs, and they turn up on new roofs and old roofs alike. That is why any inspection worth paying for looks at them first.
Most flashing problems can be fixed without touching the rest of the roof, as long as the shingles around them are still sound.
Chimneys on older brick houses deserve extra attention. Mortar joints wear, and flashing that was sealed with caulk instead of being set into the joint is a frequent cause of leaks.
If water is showing near a chimney, skylight or wall, book a flashing check. That is where we start looking.