are detrimental to fault-tolerant quantum computation and have not been rigorously treated in the existing literature. In this work, we derive the non-Markovian dynamics between TLS and qubits during a SWAP-like two-qubit gate and the associated average gate fidelity for frequency-tunable Transmon qubits. This gate dependent error model facilitates using qubits as sensors to simultaneously learn practical imperfections in both the qubit’s environment and control waveforms. We combine the-state-of-art machine learning algorithm with Moiré-enhanced swap spectroscopy to achieve robust learning using noisy experimental data. Deep neural networks are used to represent the functional map from experimental data to TLS parameters and are trained through an evolutionary algorithm. Our method achieves the highest learning efficiency and robustness against experimental imperfections to-date, representing an important step towards in-situ quantum control optimization over environmental and control defects.