A leak almost never starts where you see it
Water enters at a penetration or a flashing, runs down the underside of the decking or along a rafter, soaks insulation, and finally shows itself on a ceiling that can be several feet — sometimes a full room — away from the entry point. Wind-driven rain makes it worse: some leaks only appear when rain arrives from one direction, which is why a roof can pass three storms and fail on the fourth.
That is why chasing the stain is the wrong method. The inside of the roof deck, the attic insulation pattern, the rafter staining, and the exterior flashing details together tell you where the water actually got in.
