In this study, we report structural, vibrational, and magnetic data providing evidence of random ion displacement in the core of CdSe quantum dots on the Cd2+ sites by Co2+ ions (between x = 0 and 0.30). Structural evidence for core doping is obtained by analyzing the powder X-ray diffraction (pXRD), data which exhibits a linear lattice compression with increasing Co2+ concentration, in accord with Vegard's law. Correlated with the pXRD shift, a hardening of the CdSe longitudinal optical phonon mode and a new local vibrational mode are observed which track Co2+ doping concentration. Consistent with the observed core doping, superconducting quantum interference device (SQUID) measurements indicate a surprising increase for the onset of spin glass behavior by an order of magnitude over bulk Co:CdSe. Correlation of SQUID results, pXRD, and Raman measurements suggests that the observed enhancement of magnetic superexchange between Co2+ dopant ions in this confined system arises from changes in the nature of coupling in size-restricted materials.