This is a great example(unfortunately) of how not to do a TPO layover. The original roof was a gravel BUR system. When the layover was completed, the contractor did not ensure there would be enough slope in the new system. The result is over half of the roof holding 1-2″ of water (well after the 48 hour window, apparent from the moss).

The only solution for this will be to do a complete tear off to the deck and replace with a tapered roof system to promote positive drainage.

Make sure to always choose an experienced commercial roofing contractor to do this type of work.