Electromyographic (EMG) control relies on supervised-learning algorithms that correlate EMG to motor intent. The quality of the training dataset is critical to the runtime performance of the algorithm, but labeling motor intent is imprecise and imperfect. Traditional EMG training data is collected while participants mimic predetermined movements of a virtual hand with their own hand. This assumes participants are perfectly synchronized with the predetermined movements, which is unlikely due to reaction time and signal-processing delays. Prior work has used cross-correlation to globally shift and re-align kinematic data and EMG. Here, we quantify the impact of this global re-alignment on both classification algorithms and regression algorithms with and without a human in the loop. We also introduce a novel trial-by-trial re-alignment method to re-align EMG with kinematics on a per-movement basis. We show that EMG and kinematic data are inherently misaligned, and that reaction time is inconsistent throughout data collection. Both global and trial-by-trial re-alignment significantly improved offline performance for classification and regression. Our trial-by-trial re-alignment further improved offline classification performance relative to global realignment. However, online performance, with a human actively in the loop, was no different with or without re-alignment. This work highlights inaccuracies in labeled EMG data and has broad implications for EMG-control applications.