Water travels before it drops
Water entering at a chimney can run down a rafter for several feet before it meets a nail, a seam or a light fitting and finally comes through the ceiling. The visible damage marks where it ran out of roof, not where it got in.
So we work from the inside out and the outside in: where the staining is, where the framing runs, and what is directly uphill of it on the roof. Patching the deck above a stain is the repair that gets redone.
Boots, valleys and sidewalls
Rubber plumbing-stack boots harden and split, usually well before the shingles around them are worn. They cost very little to replace, they are a common cause of a ceiling stain in an otherwise sound roof, and they are easy to miss from the ground.
Valleys and sidewalls are the other two. A valley that was never properly lined, or a sidewall where the step flashing was replaced with a bead of sealant, will leak in wind-driven rain and stay dry in a downpour — which is exactly the intermittent leak that is hardest to pin down.
Storm damage is not always visible
Hail can take the granule layer off a shingle without cracking it. The roof looks intact from the driveway while its remaining life has been cut short, and the failure arrives a year or two later as a leak nobody connects to the storm.
Wind damage is similar: a shingle can be lifted and reseated by the next warm day with the seal strip broken underneath. It looks fine and it is no longer sealed. Both are worth documenting when they happen rather than when they leak.
When a repair is the wrong answer
A repair is right when the covering has life left and a specific detail has failed. It is the wrong answer when shingles are brittle across the whole roof, when granule loss is general rather than local, or when the same roof has already been repaired twice.
We would rather tell you that at the inspection than take the repair and have the conversation again next spring. Where it is genuinely borderline we will say that too, with what each option realistically buys you.