The strong asymmetry between electron-doped and hole-doped cuprates remains a central issue in the study of cuprate superconductors. Electron-doped cuprates are exceptionally sensitive to reductive annealing: as-grown samples are antiferromagnetic insulators, while superconductivity emerges only after the removal of roughly 1% of the oxygen content. Despite decades of investigation, the microscopic origin of this annealing effect remains unresolved, largely because conventional structural probes cannot directly detect dilute point defects in three dimensions. Here, we apply multislice electron ptychography (MEP) to La2-xCexCuO4 thin films under different annealing conditions. By combining atomic resolution, nanometer-scale depth sectioning, and single-atom sensitivity, MEP reveals a previously unrecognized point defect: an interstitial atom located adjacent to the CuO2 plane. This defect introduces a local impurity potential that is strongly detrimental to superconductivity and is largely eliminated by reductive annealing. Our findings provide a microscopic explanation for the long-standing annealing problem in electron-doped cuprates and establish a framework for the direct real-space identification of local point defects in complex oxides.