Abstract MnBi₂Te₄/(Bi₂Te₃) _n materials system has recently generated strong interest as a natural platform for the realization of the quantum anomalous Hall (QAH) state. The system is magnetically much better ordered than substitutionally doped materials, however, the detrimental effects of certain disorders are becoming increasingly acknowledged. Here, from compiling structural, compositional, and magnetic metrics of disorder in ferromagnetic (FM) MnBi₂Te₄/(Bi₂Te₃) _n it is found that migration of Mn between MnBi₂Te₄ septuple layers (SLs) and otherwise non-magnetic Bi₂Te₃ quintuple layers (QLs) has systemic consequences—it induces FM coupling of Mn-depleted SLs with Mn-doped QLs, seen in ferromagnetic resonance as an acoustic and optical resonance mode of the two coupled spin subsystems. Even for a large SL separation (n ≳ 4 QLs) the structure cannot be considered as a stack of uncoupled two-dimensional layers. Angle-resolved photoemission spectroscopy and density functional theory studies show that Mn disorder within an SL causes delocalization of electron wave functions and a change of the surface band structure as compared to the ideal MnBi₂Te₄/(Bi₂Te₃) _n . These findings highlight the critical importance of inter- and intra-SL disorder towards achieving new QAH platforms as well as exploring novel axion physics in intrinsic topological magnets.