The problem was that the installer was doing his first spray foam job ever, and the thickness of the insulation varied from zero (visible roof deck) to about 9". Unfortunately, good average thickness doesn't cut it. The coverage needs to be uniform because a lot of heat will go through the under-insulated areas. (See my article on flat or lumpy insulation performance.)
The roof must be thoroughly cleaned, and allowed to dry thoroughly. This is a critical step to ensure a successful coating application. Be careful not to damage the lap seams. Care should be taken when pressure washing not to disturb the integrity of the underlying roof membrane particularly where there are adhered seams. Refer to the specific coating manufacturer you are using for their specific requirements for roof preparation.
What do you mean by "our AC units require fresh air ventilation"? Fresh air doesn't come from the attic. If there's an atmospheric combustion appliance in the attic, such as an 80 AFUE furnace, then you shouldn't be encapsulating the attic anyway. If that's the case, you don't want spray foam on the roofline at all. You can either change out the furnace to a sealed combustion unit or do your insulating and air-sealing at the flat-ceiling level. https://www.youtube.com/watch?feature=youtube_gdata&v=ggLAUsiuI_o
Thoroughly clean the roof surface. Roofs collect oils from asphalt, chimneys, and cars plus lots of dirt and dust. Coatings don’t stick well to any of these. We recommend cleaning with an inexpensive solution of TSP or TSP Substitute in a bucket of water (follow label instructions). Use a broom to scrub ponding areas and areas of peeling coatings. Work a section at a time and hose off the dirty water. Sweep away puddles to promote drying. Do not allow wash water to dry on walls, furniture, windows, and visible surfaces. https://youtube.com/e/ggLAUsiuI_o
One of the key differentiators between traditional insulation materials and spray foam insulation is the latter’s ability to insulate and air seal. Foam insulation provides an air barrier to wherever it is applied to help mitigate air leakage from the building. Air sealing the building envelope with sprayed-in foam insulation also helps address moisture ingress to reduce the risk of mold and mildew growth as well as the formation of ice dams in colder climate zones during the winter months. When you compare foam insulation with traditional fiberglass insulation and cellulose insulation, sprayed insulation minimizes air infiltration, it assists in limiting moisture vapor from entering and escaping the home, which in turn reduces the load on heating and cooling systems. Below is a video that compares fiberglass, cellulose and open-cell spray foam in terms of insulating and air sealing value.