We isolated flux disorder effects on the transport at the critical point of the quantum magnetic field tuned Superconductor to Insulator transition (BSIT). The experiments employed films patterned into geometrically disordered hexagonal arrays. Spatial variations in the flux per unit cell, which grow in a perpendicular magnetic field, constitute flux disorder. The growth of flux disorder with magnetic field limited the number of BSITs exhibited by a single film due to flux matching effects. The critical metallic resistance at successive BSITs grew with flux disorder contrary to predictions of its universality. These results open the door for controlled studies of disorder effects on the universality class of an ubiquitous quantum phase transition.