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The gapped Dirac-like surface states of magnetic topological insulator MnBi_2-xSb_xTe₄ (MBST) are a promising host for exotic quantum phenomena such as the quantum anomalous Hall effect and axion insulating states. However, it has become clear that atomic defects undermine the stabilization of such quantum phases as they lead to spatial variations in the surface state gap and doping levels. The large number of possible defect configurations in MBST make studying the influence of individual defects virtually impossible. Here, we present a statistical analysis of the nanoscale effect of defects in MBST by scanning tunneling microscopy/spectroscopy (STM/S). We identify (Bi,Sb)_Mn anti-site defects to be the main source of doping fluctuations, resulting in the formation of nanoscale charge puddles, while Mn_(Bi/Sb) anti-site defects are the main source of fluctuations in the surface state gap. Our findings can guide further optimization of this material system via defect engineering.