Small nail holes left behind from old vents satellite dish brackets or anything previously attached to the roof can allow water to enter and cause damage for years before leaking is noticed.
How to repair leaky roof flashing.
Start low soaking the area just above where the leak appears in the house.
If a leak is difficult to find enlist a helper and go up on the roof with a garden hose.
Use a roofing nail to keep the section down and apply some caulking around the edge to seal against water.
For example soak the downhill side of a chimney first then each side then the top on both sides.
Spread some roofing tar under the edge that is sticking up and bend it back down to a flat surface.
First roughen the area around the hole with a wire brush or sandpaper and then clean it.
Clean the surface of the roof under the flashing.
Isolate areas when you run the hose.
Plug pinholes with roofing cement and patch holes up to about 3 4 inch in diameter with a patch from the same material as the flashing.