Should I be worried about the water pooling on my flat EPDM material r

Hi, I've had a flat roof extension built which completed about 6 months ago. The builder used EPDM material for the roof covering. I also had 2 skylights installed at the same time - on raised timber kerbs, each skylight is about 80cm away from the wall on the floor above. Behind one skylight it's fine, behind the other water pools after raining and stays there for a long time until it dries out and I can already see moulding green. My builder says he put curves in so the water runs away but can't see much of a curve on the side with the water issue. And he advises me that it won't be a problem as the material is fully sealed Can you advise on this? Is this something to worry about and what remediation can I ask the builder to do? Note: I can already see a few bobbles elsewhere on the roof covering Thanks