There are many reasons why this could be happening.  The most common culprits are a) your skylights, chimney or lead boots may need reflashing; b) you may have blown off shingles from wind storms that are now exposing your roof to the elements; or, c) you have nail pops.  Nail pops refer to a condition established at the time of original installation or during a previous repair.  The nails entered an existing hole or in between two pieces of plywood and did not "grab" the wood.  As the roof heats and cools, the nail will raise up and cause the shingle to form a bump. As the expansion and contraction continues the nail eventually pokes a hole through the shingle and causes a leak.