Yes.  If a contaminated or alternative refrigerant is used–knowingly or unknowingly –the original factory warranties on the A/C system (including components, i.e, compressor, evaporator, etc.) typically are voided.  Additionally, the warranty on the A/C service equipment that the technician used is also voided, in most cases.

Whoever placed the refrigerant into the car or into the machine is responsible.  In the event that a technician contaminated a customer's A/C system, the technician/shop pays for the repair –in the event that a technician pulled contaminated refrigerant through a recovery/recycling machine, again, the technician or shop pays for the repair!