Various scenarios of measurements of electric dipole moment (EDM) of light hadrons with the use of a storage ring were proposed. Most of these methods are based on the measurement of the vertical spin component for an initially horizontal polarized beam. Since the expected EDM effect is very small, one has to pay attention to various sources of systematic uncertainties. One of the most important sources are misalignments of the magnets forming the storage ring lattice, which may produce an effect that mimics an EDM. This false signal could be much larger than the expected EDM signal, even for very small magnet misalignments. This paper describes a novel method for the determination of the contribution of magnets misalignments to the expected EDM signal. It is shown that the magnitude of this effect could be estimated via a Fourier analysis of the time-dependent vertical polarization. This could be achieved by sampling the vertical polarization with a frequency larger than the beam revolution frequency, which corresponds to polarization measurements in at least two positions in the storage ring. The presented method can be applied to any scenario proposed for EDM measurements using a storage ring.