The Dirac point gap at the surface of the antiferromagnetic topological insulator MnBi$_2$Te$_4$ is a highly debated issue. While the early photoemission measurements reported on large gaps in agreement with theoretical predictions, other experiments found vanishingly small splitting of the MnBi$_2$Te$_4$ Dirac cone. Here, we study the crystalline and electronic structure of MnBi$_2$Te$_4$(0001) using scanning tunneling microscopy/spectroscopy (STM/S), micro($mu$)-laser angle resolved photoemission spectroscopy (ARPES), and density functional theory (DFT) calculations. Our topographic STM images clearly reveal features corresponding to point defects in the surface Te and subsurface Bi layers that we identify with the aid of STM simulations as Bi$_text{Te}$ antisites (Bi atoms at the Te sites) and Mn$_text{Bi}$ substitutions (Mn atoms at the Bi sites), respectively. X-ray diffraction (XRD) experiments further evidence the presence of cation (Mn-Bi) intermixing. Altogether, this affects the distribution of the Mn atoms, which, inevitably, leads to a deviation of the MnBi$_2$Te$_4$ magnetic structure from that predicted for the ideal crystal structure. Our transport measurements suggest that the degree of this deviation varies from sample to sample. Consistently, the ARPES/STS experiments reveal that the Dirac point gap of the topological surface state is different for different samples/sample cleavages. Our DFT surface electronic structure calculations show that, due to the predominant localization of the topological surface state near the Bi layers, Mn$_text{Bi}$ defects can cause a strong reduction of the MnBi$_2$Te$_4$ Dirac point gap, given the recently proved antiparallel alignment of the Mn$_text{Bi}$ moments with respect to those of the Mn layer. Our results provide a key to puzzle out the MnBi$_2$Te$_4$ Dirac point gap mystery.
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