In this study, the magnetoresistance measurements of Se-deficient (i.e., NbSe1.85) as well as Fe-incorporated NbSe2 (Fe0.0015NbSe2) were performed to observe the effect of both intrinsic and extrinsic defect in the thermally activated flux flow region (TAFF) of NbSe2. In TAFF region, NbSe1.85 shows nonlinear response of thermal activation energy (TAE) with temperature following the modified TAFF method. For NbSe2 and Fe0.0015NbSe2, TAE depends linearly on temperature and hence was evaluated using Arrhenius relation. NbSe1.85 can be considered as the 2D-like system in the TAFF region. The magnetic field dependence of TAE shows parabolic nature in Fe0.0015NbSe2 in contrast to the power-law dependence of TAE in NbSe1.85. The power-law dependence of TAE in NbSe1.85 indicates the plastic deformation flux lines. The parabolic dependence indicates the elastic deformation of flux lines in pure as well as in Fe0.0015NbSe2. The band structures and density of states (DOS) of the above mentioned two cases were calculated using first-principle density functional theory. The number of bands and the DOS at the Fermi level decreases remarkably for both Se vacancy and Fe doping cases, indicating to the degradation of superconductivity. A peak shift in the partial density of state of Nb was observed at the Fermi level of Fe0.0015NbSe2. Spin-polarized optimization of first-principle calculations implies large Fe-Se overlaps and contradicts the Kondo mechanism due to the low concentration of Fe atoms. The spin polarization calculation indicates the negligible effect of magnetism of Fe atoms in Fe0.0015NbSe2.