Ion-trap quantum computers offer a large number of possible qubit couplings, each of which requires individual calibration and can be misconfigured. To enhance the duty cycle of an ion trap, we develop a strategy that diagnoses individual miscalibrated couplings using only log-many tests. This strategy is validated on a commercial ion-trap quantum computer, where we illustrate the process of debugging faulty quantum gates. Our methodology provides a scalable pathway towards fault detections on a larger scale ion-trap quantum computers, confirmed by simulations up to 32 qubits.