Velocity fluctuations, measured via multi-wire probes, are very sensitive to misalignment between the calibration coordinate system and that of the wind tunnel. The present study proposes a scheme to correct the erroneous velocity fluctuations processed from a misaligned calibration while investigating a wall-bounded turbulent shear flow. The scheme is based on the premise that the viscous-scaled spectral energy distribution in the small-scales is invariant with Reynolds number and solely depends on the viscous-scaled spatial resolution of the sensor. Energy spectra processed from the misaligned calibration, in this small-scale range, are compared with the ‘expected’ spectra obtained via synthetic experiments on a direct numerical simulation data set. The erroneous lateral velocity spectra is found to be either relatively amplified or attenuated, by almost the same factor, at all wall-normal distances across the shear flow. A unique gain, defined to be the correction ratio, is thus obtained by forcing the erroneous spectra onto the reference spectra in this scale range. This ratio is further used to rectify the time series of the lateral velocity fluctuations, acquired across the shear flow, via Fourier analysis. The scheme is shown to be effective for experiments conducted across a decade of Reynolds number and using probes of varying spatial resolution.