The cricket is way too short especailly on the right side of the scupper, thats part of the reason why you have a ponding/debris issue. If we are talking about design, there is also not an overflow scupper which would worry me if I were living in that house.
Okay, here is the biggest tip that your intersection at the transition area from the flat roof to the scupper side parapet wall is leaking, even if ever so slightly.
Do you see how the rest of the roof area is dry, but just above the flat roof right on the bottom of the parapet wall, mostly to the right of the scupper, is still wet looking. There is trapped moisture behind those base flashing materials. You more than likely have stress cracks running horizontally to the flat roof right there. They do not have to be wide open fissures to leak, just dried our and cracked material.