Identify the surface
Felt, EPDM, GRP and asphalt need different repair materials. A general waterproof coating is not automatically compatible.
Look at ponding
A small amount of water after rain is one thing. A deep pond that remains for days can point to poor falls, a blocked outlet or sagging deck.
Edges fail differently from the field
Upstands, trims, corners and penetrations move and weather in their own way. A small opening at one edge can wet a large area below.