Many leak problems begin when water makes it way under gaps in the skylight itself, into the flashing around the skylight, or the flat roof membrane that goes up the curb. When this water freezes, it expands causing the gap to expand. After a few seasons of this expansion and contraction, the skylight will start to leak.
Another cause of skylight problems is improper installation. Improper flashing installations accounts for the large majority of skylight problems which is why it is always recommended that a professional install any type of skylight.
Other common problems that can come from skylights include condensation from poor insulation, too much heat, mold or mildew from constant dampness, roof membrane can rot and air can get in resulting in decreased energy efficiency.