Understanding defects in Cu(In,Ga)(Se,S)2 (CIGS), especially correlating changes in the film formation process with differences in material properties, photovoltaic (PV) device performance, and defect levels extracted from admittance spectroscopy, is a critical but challenging undertaking due to the complex nature of this polycrystalline compound semiconductor. Here we present a systematic comparative study wherein varying defect density levels in CIGS films were intentionally induced by growing CIGS grains using different selenium activity levels. Material characterization results by techniques including X-ray diffraction, scanning electron microscopy, transmission electron microscopy, secondary ion mass spectrometry, X-ray photoelectron spectroscopy, and medium energy ion scattering indicate that this process variation, although not significantly affecting CIGS grain structure, crystal orientation, or bulk composition, leads to enhanced formation of a defective chalcopyrite layer with high density of indium or gallium at copper antisite defects ((In, Ga)Cu) near the CIGS surface, for CIGS films grown with insufficient selenium supply. This defective layer or the film growth conditions associated with it is further linked with observed current-voltage characteristics, including rollover and crossover behavior, and a defect state at around 110 meV (generally denoted as the N1 defect) commonly observed in admittance spectroscopy. The impact of the (In, Ga)Cu defects on device PV performance is also established.