Roofs are sometimes found leaking where the chimney stack protrudes through the roof.  Home owners and amateurs sometimes attempt to install the necessary metal flashing needed to prevent water from penetrating behind the siding or brick on the stack. Step flashing should be installed under each individual row of shingles extending up the sides of the stack. Counter flashing or siding is then installed on top and down the sides of the step flashing. 

The flashing pictured has been incorrectly installed on top of the shingles. Water damage was also found in the attic below this area.

Franklin TN_incorrect installed_chimney stack flashing