Superconducting qubits are among the most advanced candidates for achieving fault-tolerant quantum computing. Despite recent significant advancements in the qubit lifetimes, the origin of the loss mechanism for state-of-the-art qubits is still subject to investigation. Furthermore, the successful implementation of quantum error correction requires negligible correlated errors between qubits. Here, we realize long-lived superconducting transmon qubits that exhibit fluctuating lifetimes, averaging 0.2 ms and exceeding 0.4 ms - corresponding to quality factors above 5 million and 10 million, respectively. We then investigate their dominant error mechanism. By introducing novel time-resolved error measurements that are synchronized with the operation of the pulse tube cooler in a dilution refrigerator, we find that mechanical vibrations from the pulse tube induce nonequilibrium dynamics in highly coherent qubits, leading to their correlated bit-flip errors. Our findings not only deepen our understanding of the qubit error mechanisms but also provide valuable insights into potential error-mitigation strategies for achieving fault tolerance by decoupling superconducting qubits from their mechanical environments.|Significant efforts have been dedicated to understanding the mechanisms of decoherence in superconducting qubits. Here, using time-resolved error measurements, the authors link errors present in transmon qubits based on Nb electrodes to mechanical vibrations of a commonly used pulse tube cooler.