Even a flat roof is suppossed to drain. This is a torchdown roof and you will see a big puddle. That is called ponding. Fact is, that is a low place and, because of the lack of slope toward built in drains, the water stays on the roof. Water like that, on a roof, will almost always eventually lead to a leak below.
The photo below is a snapshot of the area directly below the pond that you see above.
Bottom line -- Flat roof or not, you want the water to drain off the roof in a reasonable period of time. Time to call a roofer.
Steven L. Smith
Bellingham WA Home Inspections