the origin of the loss mechanism for state-of-the-art qubits is still subject to investigation. Moreover, successful implementation of quantum error correction requires negligible correlated errors among qubits. Here, we realize ultra-coherent superconducting transmon qubits based on niobium capacitor electrodes, with lifetimes exceeding 0.4 ms. By employing a nearly quantum-limited readout chain based on a Josephson traveling wave parametric amplifier, we are able to simultaneously record bit-flip errors occurring in a multiple-qubit device, revealing that the bit-flip errors in two highly coherent qubits are strongly correlated. By introducing a novel time-resolved analysis synchronized with the operation of the pulse tube cooler in a dilution refrigerator, we find that a pulse tube mechanical shock causes nonequilibrium dynamics of the qubits, leading to correlated bit-flip errors as well as transitions outside of the computational state space. Our observations confirm that coherence improvements are still attainable in transmon qubits based on the superconducting material that has been commonly used in the field. In addition, our findings are consistent with qubit dynamics induced by two-level systems and quasiparticles, deepening our understanding of the qubit error mechanisms. Finally, these results inform possible new error-mitigation strategies by decoupling superconducting qubits from their mechanical environments.