I’ve seen many SPF roofs, but not that particular defect. It sure looks like the foam was touched prior to it fully curing.
That said there are lots of weird things in the world, I’d want more evidence it’s SPF.
I agree with @mtimpani that the solution is sikiflex or some other caulk, then a new layer of elastomertic roof coating.
The salespeople will tell you SPF is closed cell and can’t get wet. This is… wrong. It gets saturated but slowly.