The drip is rarely under the hole
A flat roof leak is hard to pin down. On a sloped roof, water runs down and out. On a flat roof, it can get in at one spot and travel. It runs along the steel deck, soaks into the insulation, and drips out wherever it finds a low seam. The bucket in aisle 12 may be catching water from a hole 30 feet away.
That is why so many leaks come back after a quick patch. The patch went over the drip, not the entry point. In the Kansas City metro, where hard spring storms and cold winters work on the same roof, a leak that is not traced tends to grow.