Here, we investigate the impact of the intrinsic properties of two-dimensional transmon qubits on quasiparticle tunneling (QPT) and discuss how we can use QPT to gain critical information about the Josephson junction quality and device performance. We find the tunneling rate of the non-equilibrium quasiparticles to be sensitive to the choice of the shunting capacitor material and their geometry in qubits. In some devices, we observe an anomalous temperature dependence of the QPT rate below 100 mK that deviates from a constant background associated with non-equilibrium quasiparticles. We speculate that high transmission sites within the Josephson junction’s tunnel barrier can lead to this behavior, which we can model by assuming that the defect sites have a smaller effective superconducting gap than the leads of the junction. Our results present a unique characterization tool for tunnel barrier quality in Josephson junctions and shed light on how quasiparticles can interact with various elements of the qubit circuit.