Are you sure that the problem is with silicon or just a waxy residue. they can give the same reaction. If its silicon then the paintshop will also have a problem if this has been made airborne.
Was the car taken in ready to paint or did the body shop do all of the prep. If its the latter then the problem should have been picked up in either the etch or primer stages, and in no circumstances should the top coat have been applied if there was a known problem. If the bodyshop saw no evidence of silicon/wax in the primer then the problem clearly lies with their premesis or someone has contaminated the primed surface. Believe me silicon can shut down a paintshop as its so difficult if not impossible to remove from a spray booth. You can decontaminate to an extent with anti silicon aditives in the paint but really once its there its there for good.
You should return the car to the bodyshop immediately and demand an explanation if what I describe above has been the case. Really you should not have touched the car, and definately not cut back the paint. Still, if the bodyshop cannot explain why the silicon/wax could not be removed with panel wipe, and /or if it was present in the primer then I would be suggesting that they might have been negligent in the final prep.
Reading back through your description I assume that the paintwork has lots of sink marks/small craters in the surface, this is wax, if you have raised parts in the surface then this is dust or airborne particles. Can you clarify which problem you have. Once this is clear I may be able to shed a bit more light on the matter
