Many homes will have minor roof leaks from a type of flashing called the furnace flue jack. This is a completely
avoidable leak. Sometimes roofing contractors will remove the storm collar and install a bead of caulk between the furnace flue and the jack. This is a very temporary fix and will leak as soon as the caulk disintegrates. The next time you get a chance, look up on your roof (with binoculars) and make sure the your storm collar(s) is properly installed. Or call your favorite home inspector and order a maintenance inspection.