Roof leaks are a relatively common occurrence. However 70% of all roof leaks are due to flashing or valley failures. Any leaking should cause you to evaluate the possibility that the problem is due to flashing and/or valley's before the roof is assumed to be a problem.
After some time, caulking or fasteners may begin to loosen and deteriorate. When this occurs, rain may enter small openings or cracks and penetrate beneath the flashing. This will allow the rain to make contact with the wood sheathing or framing members of the house. Once this occurs, if not corrected, deterioration of the sheathing or framing will result.