Skylight leaks are one of the most common type of leak on a roof.
There are many reasons why skylights are vulnerable. Some causes are quite obvious and some are harder to pin down...
First hand experience:
I have a large skylight and it is installed on a terracotta tiled roof. It provides good natural light and for many years, it stayed dry during the heaviest of storms. Then one day when it was raining quite heavily, water was pouring down the ceiling at the side of the skylight...
I do not do emergency repairs in the rain - but in this instance, I made an exception to the rule. It was tricky on the wet tiles even after I waited for the rain to die down to a drizzle before attempting a fix.
I unseated the roof tiles from the side of the skylight and got a real appreciation of the role that leaves and dirt can play in blocking the flow of water on a skylight underflashing. Leaves and debris had built up over time and had were jammed against the underside of the roof tile where it rested on the flashing. This caused a 'damming effect' - and diverted the flow of water over the lip of the flashing into the ceiling cavity.
It was a simple matter then of removing the debris and the skylight has been fine ever since.
So, if you get a sudden downpour from the side of your skylight, then it will be leaves causing the problem. Sometimes, the skylight leak suddenly stops again as the rain continues to fall. This indicates that the leaves have been dislodged by the water flow and is no longer an obstruction.
This can be a source of frustration on the poor roofer who gets called out to investigate the skylight leak and find that everything looks ok - simply because the obstruction had cleared itself and there was no evidence left behind.
The video below shows exactly how the leaves can cause the obstruction:
A persistent seepage from the skylight surrounds.
A small (but persistent) leak at a skylight usually means a faulty skylight, a faulty skylight installation - or a minor blockage.