Shortly after buying a mid-century split-level in the Pacific Northwest I had the old torch-down flat roof replaced with a PVC membrane. As half of the top level has a vaulted ceiling without much room for additional insulation above it, 3 inches of ISO rigid foam insulation were added on top of the roof deck. The insulation was added on the half having a shallow attic as well as the vaulted half. On the side with the attic, the roofers cut through the insulation to install roof vents. Let's suppose, for the sake of argument, that it was reasonable to place the insulation over both halves of the roof (as opposed to only placing it over the vaulted half and then, say, blowing in more insulation in the attic for less money per R-factor). Should the vents have been added? At the time, I assumed the venting was a necessary compromise between energy conservation and humidity dissipation, much like the ventilation that's needed in sealed homes. But, upon further consideration, it seems like the right thing to have done would have been to block the soffit vents, leveraging the new insulation's ability to prevent condensation beneath the roof deck.
You are absolutely right. The kind of roof you describe does not need to be vented, and in fact cannot be vented without compromising all the polyiso insulation you had added (that was a good idea!). The roofers have damaged your insulation layer and put your roof at risk. Call them back and make them fix it. If they won't, call the contracting board.