Mn, Fe, and Cu ions, when doped into ZnO nanocrystals, impart magnetic phenomena to their semiconducting property. Although notable in the dilute magnetic semiconductor community, transition metal (TM) ion-doped ZnO lacks investigations that inform researchers on the local lattice structure around the dopant ion, its spin-exchange phenomena, and the interaction between its intrinsic defects and the doped metal ion. The current study presents a detailed multi-frequency (X- and Q-band) EPR investigation that clarifies the localization of the dopant ion, its site symmetry, and the formation of intrinsic-extrinsic defect complexes in ZnO:TM. The incorporation of TM ion is observed to modify the intrinsic defect structure of ZnO nanocrystals. Particularly, a deviation from the core-shell model is observed for ZnO:TM, and the appearance of intrinsic-extrinsic defect complexes that may contribute to a peculiar spin-exchange phenomenon are noticed. Additionally, the localization as observed from the resonance lines of defect complexes comprising Cu2+ is different from those of Mn2+ and Fe3+, showing charge selective substitutions in the matrix.