A metamaterial is a periodic structure which can be considered as an effective medium that exhibits an atypical response for a corresponding range of electromagnetic (EM) waves. For metamaterial absorbers (MMA) working in the GHz regime, the frequency-domain-measurement setup consisting of two horn antennas connected to a network analyzer is widely used. The absorption spectra obtained with this setup usually exhibits some periodic fluctuation (PF) across the entire range of measurement. Typically, this PF in the frequency-domain spectrum is ignored because it is distinct from major features and has a small amplitude. We have examined the PF through a finite-difference time-domain (FDTD) simulation in order to verify the validity of such assumption. We concluded that the PF is caused by a part of EM wave radiated by an antenna (source), and directly propagating to another (detector), resulting in an interference between this leaked EM wave and the one reflected from the sample. We have successfully reproduced the periodic fluctuation of the experimental spectra by FDTD simulation. We examined the angle of incidence dependence. The amplitude increases because the amount of leaked EM waves increases, while the periodicity increases because the distance between the two antennas increases, resulting in a shortened path difference. We conclude that the PF is a systematic error which can be safely ignored.