An analysis of Mn substitution in SrTiO3 is performed in order to understand the origin of reported spin coupling in lightly Mn-doped SrTiO3. The spin glass state magnetoelectrically coupled to the dipolar glass state has previously been reported for SrTiO3 substituted with only 2% of Mn on the B-site. An analysis of the substitution mechanism for A- and B-site doping shows a strong influence of processing conditions, such as processing temperature, oxygen partial pressure, and off-stoichiometry. The required conditions for a site-selective substitution are defined, which yield a single-phase and almost defect-free perovskite. Magnetic measurements show no magnetic anomalies resulting from spin coupling and only a simple paramagnetic behavior. Magnetic anomalies are observed only for the samples in which Mn is misplaced within the cation sublattice of the SrTiO3 perovskite. This occurs due to improper material processing, which causes initially unpredicted changes in the valence state of the Mn and results in the formation of structural defects and irregularities associated with segregation and nucleation of the magnetic species. Previously reported spin coupling in Mn-doped SrTiO3 is not an intrinsic phenomenon and cannot be treated as a spin glass.