Start above the window
A broken slate or tile further up can feed water onto the window flashing. Moss can also gather above the top flashing and slow drainage.
Flashing kits are shaped for the covering
A kit for flat slate is different from one intended for a deep-profile tile. Poorly fitted side pieces or a badly dressed top section can admit rain even when the window itself is fine.
Condensation looks convincing
Water on the inside frame after showers or on cold mornings can run onto the reveal. If it happens in dry weather, investigate humidity and ventilation before arranging roof work.
Do not seal the drainage channels
Modern roof windows are designed to drain water around the frame. Filling channels with sealant can create another problem. Repair the failed detail rather than closing every visible gap.