Vents on fibreglass flat roof

[notonyournelly]

Flat roof just been laid and leaks around the vents,mushroom type, roofer put them in after fibreglass but should he have put them in before and fibreglass and fibreglassed around them along with the roof, also is it OK for him to redo them with ct1 and fibreglass,,,,hope this is clear,,,,also there isnt a run off and water pools on roof,