The hole was not in the center of the unit, the flashing was not pushed up a good shingle tab length up toward the ridge. Roofing nails could have punctured the flashing causing a leak at that point, proper caulking was not done.
I hate to say this, but these roof things are so basic easy IF ALL procedures are followed when mounting them. Somewhere along the way, something was done wrong and here you are.
Do as I am sure Jay will say, take pictures, document all communications, save paper work, and take pictures of the thing leaking with the tub of water below. Get results through gentleman channels, when that fails, you will have a good docia of evidence.