This document describes a method for detecting systematic errors in femtosecond laser two-pulse trains using spectral analysis. Laser pulses are shaped into phase-locked two-pulse trains and background spectra are collected at varying pulse delays and phases. A MATLAB script calculates theoretical spectra and compares them to experimental data to screen for errors. The analysis revealed a 5% systematic error in the programmed pulse delay, suggesting calibration of the pulse shaper is needed. The method can help automate error detection and indication of necessary recalibration.