Myth busted about standing water on a rubber roof - see the plants grow in this pond 

I always find people that are concerned about ponding or standing water on a rubber roof. I have come across many roofs where water has been pooling for such a long time that plants started to grow. If a rubber membrane is torched properly then it should be able to hold water indefinitely.
EPDM Rubber seams can separate if it is submerged under for a long period of time. I think the best type of membranes to be used for pool liners or where water is pooling, is TPO or PVC. In the video, the water has been pooling on a Modified Bitumen Torch Down Rubber membrane for a long time.
Although it is best practice not to have standing water on a flat roof. But if there is some pooling then there is no need to be alarmed unless it starts leaking because the roof was not installed correctly.
Ponding water on a flat roof should be avoided because it provided a breeding ground for mosquitos and freezing in winter adds stress to the roof itself.