  The van der Waals compound, MnBi$_2$Te$_4$, is the first intrinsic magnetic
topological insulator, providing a materials platform for exploring exotic
quantum phenomena such as the axion insulator state and the quantum anomalous
Hall effect. However, intrinsic structural imperfections lead to bulk
conductivity, and the roles of magnetic defects are still unknown. With higher
concentrations of same types of magnetic defects, the isostructural compound
MnSb$_2$Te$_4$ is a better model system for a systematic investigation of the
connections among magnetic, topology and lattice defects. In this work, the
impact of antisite defects on the magnetism and electronic structure is studied
in MnSb$_2$Te$_4$. Mn-Sb site mixing leads to complex magnetic structures and
tunes the interlayer magnetic coupling between antiferromagnetic and
ferromagnetic. The detailed nonstoichiometry and site-mixing of MnSb$_2$Te$_4$
crystals depend on the growth parameters, which can lead to $\approx$40\% of Mn
sites occupied by Sb and $\approx$15\% of Sb sites by Mn in as-grown crystals.
Single crystal neutron diffraction and electron microscopy studies show nearly
random distribution of the antisite defects. Band structure calculations
suggest that the Mn-Sb site-mixing favors a FM interlayer coupling, consistent
with experimental observation, but is detrimental to the band inversion
required for a nontrivial topology. Our results suggest a long range magnetic
order of Mn ions sitting on Bi sites in MnBi$_2$Te$_4$. The effects of site
mixing should be considered in all layered heterostructures that consist of
alternating magnetic and topological layers, including the entire family of
MnTe(Bi$_2$Te$_3$)$_n$, its Sb analogs and their solid solution.
