Recently, various fundamental properties of GaPS4 such as anisotropy and strain-induced properties have been reported, but the impacts of the stacking sequence in layered materials remain ambiguous. This ambiguity is evident in the inconsistent Raman scattering data reported for GaPS4, suggesting a significant influence of stacking order on its physical properties. To demonstrate the discrepancies, this study investigates the vibrational characteristics of 2D GaPS4 under different stacking sequences using both experimental observations and theoretical models (AA and AB sequences) through density functional theory calculations. The results of our theoretical calculations revealed that the identical stacking sequence structure significantly influences the vibrational configurations of GaPS4, which results in divergent configurations of Raman scattering spectra including unidentified Raman peaks. Our study addresses not only the clarification of the ambiguity of experimental observations but also qualitative criteria to evaluate the degree of each stacking sequence.