The competition between corner-, edge-, and face-sharing octahedral networks is a cause of phase inhomogeneity in metal halide perovskite thin-films. Here we probe the charged iodine vacancy distribution and transport at the junction between cubic and hexagonal polytypes of CsPbI3 from first-principles materials modeling. We predict a lower defect formation energy in the face-sharing regions, which correlates with a longer Pb–I bond length and causes a million-fold increase in local defect concentration. These defects are predicted to be more mobile in the face-sharing regions with a reduced activation energy for vacancy-mediated diffusion. We conclude that hexagonal phase inclusions or interfaces will act as defect sinks that could influence carrier dynamics in perovskite-based solar cells and electrical devices.