<p>Magnetic quantum oscillations, such as Shubnikov-de Haas oscillations or de Haas-van Alphen oscillations, are widely used tools for fermiology. Notably, the phase of magnetic quantum oscillations could inform about the symmetry or topology of materials with careful analysis. However, the interpretation of the phase is usually much more subtle than that of the frequency, and unexpected phases are often observed, hindering the extraction of intrinsic information from the phases. Therefore, identifying the possible source of phase deviation is crucial for the proper interpretation of the phase. Here, we grew high-quality NbSb₂ single crystals with the exceptionally low residual resistivity of ~0.078 μΩ cm at <i>T</i> = 2 K, which enables us to detect the effect of a tiny amount of impurities in the de Haas-van Alphen effect. Unexpectedly, we observed a significant phase deviation around 0.58π induced by magnetic impurities, but no phase shift by nonmagnetic impurities. We explained the phase deviation by the modified Lifshitz-Kosevich formula incorporating magnetic scattering or spin-dependent scattering, which is supported by the imbalanced density of states between spin-up and -down impurity states calculated by the density functional theory. Our study showcases the effect of a tiny amount of magnetic impurities on the phase of magnetic quantum oscillations, giving an insight into the phase analysis and understanding the interaction between itinerant electrons and magnetic impurities.</p>