Artificial solids composed of semiconductor quantum dots (QDs) are being developed for large-area electronic and optoelectronic applications, but these materials often have defect-induced in-gap states (IGS) of unknown chemical origin. Here we performed scanning probe based spectroscopic analysis and density functional theory calculations to determine the nature of such states and their electronic structure. We found that IGS near the valence band occur frequently in the QDs except when treated with reducing agents. Calculations on various possible defects and chemical spectroscopy revealed that molecular oxygen is most likely at the origin of these IGS. We expect this impurity-induced deep IGS to be a common occurrence in ionic semiconductors, where the intrinsic vacancy defects either do not produce IGS or produce shallow states near band edges. Ionic QDs with surface passivation to block impurity adsorption are thus ideal for high-efficiency optoelectronic device applications