The most common issue that causes torch down roofs to fail is improper sealing around the edge metal flashing or pipe and vent flashings. Water often penetrates the roof due to a lack of adhesion of the torch down material to the edge metal. Water can leak through the ceiling and walls and migrate into the house.
If the roof is new, you can patch it without problem. If it is already 15 years old, the roof should be replaced.
Proper patches must be thoroughly cleaned and prepared. If improperly patched, a weak spot develops at the seam.