I have seen them before and sometimes its impossible to figure out. The first thing I look for is an exposed nail or a hole in a shingle. I see many like that where scaffold brackets were nailed through shingles, but they are always close to edges. Sometimes it can be water traveling down from above or from a nearby valley, but then usually would enter at a seam. Could have entered through a nail hole in the sheathing that it not in the roofing.