Interfaces between topological insulators (TIs) and magnetic materials, including 2D van der Waals magnets, are currently generating enormous interest, due to phenomena such as the quantum anomalous Hall effect. Many of the magnets employed contain reactive and diffusive elements such as Mn, however, raising serious materials challenges. This work explores the interface between BiSe and Mn and MnSe, revealing chemical and electronic changes at the interface depending on how Mn is deposited. Mn deposited without excess selenium shows Se out-diffusion from BiSe to the Mn. Supplying excess Se alongside Mn prevents this Se out-diffusion, but the interface becomes affected by a negative surface dipole. This dipole forms due to preferential creation of -MnSe(111) over the 1T-MnSe phase. This study shows that chemical diffusion and dipole formation are important for Mn-BiSe and MnSe-BiSe interfaces and must generally be considered at TI/Mn chalcogenide interfaces.