My roof, my roof is on fire

Well not on fire, but flooding. The newest part of our addition has sprung a leak underneath the recessed lighting. Water is coming out of the light fixture and we called the contractor who told us that it's not the roof's fault, but the wind driven rain. Crapstick totally buys this, but I thought the roof was supposed to protect against the rain. Huh? I need a roofing education.