I have seen plenty that leak, but the problems are in the detailing not the fact that it is a flat roof.
Take your typical box store, a Walmart or a Home Depot. 60,000 to 120,000 sqft of flat bellybutton roof and leaks are unacceptable. Skylights just leak, period.
Now the flip side of that, is a typical residence or "architectural" commercial structure. The roof is not a big flat square, it is cut up into smaller areas. The corners and penetrations increase in both number and complexity. So do the leaks.
All that said, water penetration into the walls is a given, and should be planned for in the design. This is where it becomes a problem, when you have an iffy roofing system and a poorly designed wall section.