In this paper, we investigated the low-temperature lattice dynamics in two GeTe crystals with varying Ge defect stoichiometry. The X-ray Diffraction (XRD) of the as-cleaved ingots indicate that the orientation is mainly along the h0l direction. From the Raman spectra, a comparison of the linewidth variation with temperature for the in-plane (E-mode) vibrations reveals a subtle enhancement around 170 K for the less stoichiometric crystal, depicting a more anharmonic nature, via the 4-phonon scattering processes. Furthermore, a comparison of the out-of-plane A_T^1 mode indicates a sensitivity of a weaker Raman signal ( about 239 cm -1) from disordered GeTe4 tetrahedra that has adversely affected the mode dynamics in the less stoichiometric sample (S1). However, this weaker signal is not observed for the more stoichiometric sample (S2) below 200 K. The Machine Learned Molecular Dynamics (MLMD) simulations performed to calculate the phonon spectral densities reveal that the heavier atom, Te dominate below 100 cm-1, while, the lighter Ge has more significant contribution above 100 cm-1. Thus, the change observed only in the 120 cm-1 (A_T^1) mode is justified by defects at the Ge sites. Specific heat capacity measurements are performed that show a broad hump near 14 K, when plotted as Cp/T^3 versus T indicative of a non-Debye nature. Hence, considering the two optical modes in the Raman spectra, a Debye and two-Einstein modes model is conceptualized to explain the low-temperature specific heat. These calculations reveal a softer bonding vis-a-vis lowering of Debye temperature in S1. Lower Einstein temperatures are also observed in S1, which is attributed to the easy activation of these localized modes that affect the harmonicity of the lattice. Finally, the low-temperature resistivity measurements reveal a reduction in the effective phonon frequency (w_e) through the estimation of Te.