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Oriented attachment of colloidal quantum dots allows the growth of two-dimensional crystals by design, which could have striking electronic properties upon progress on manipulating their conductivity. Here, we explore the origin of doping in square and epitaxially fused PbSe quantum dot superlattices with low temperature scanning tunneling microscope and spectroscopy. Probing the density of states of numerous individual quantum dots reveals an electronic coupling between the hole ground states of the quantum dots. Moreover, a small amount of quantum dots shows a reproducible deep level in the band gap, which is not caused by structural defects in the 2 connections but arises from unpassivated sites at the {111} facets. Based on semiconductor statistics, these distinct defective quantum dots, randomly distributed in the superlattice, trap electrons, releasing a concentration of free holes, which is intimately related to the interdot electronic coupling. They act as acceptor quantum dots in the host quantum dot lattice, mimicking the role of dopant atoms in a semiconductor crystal.