X-ray photoelectron spectroscopy (XPS) and resonant x-ray emission spectroscopy (RXES) measurements of pellet and thin film forms of TiO$_2$ with implanted Fe ions are presented and discussed. The findings indicate that Fe-implantation in a TiO$_2$ pellet sample induces heterovalent cation substitution (Fe$^{2+}rightarrow$ Ti$^{4+}$) beneath the surface region. But in thin film samples, the clustering of Fe atoms is primarily detected. In addition to this, significant amounts of secondary phases of Fe$^{3+}$ are detected on the surface of all doped samples due to oxygen exposure. These experimental findings are compared with density functional theory (DFT) calculations of formation energies for different configurations of structural defects in the implanted TiO$_2$:Fe system. According to our calculations, the clustering of Fe-atoms in TiO$_2$:Fe thin films can be attributed to the formation of combined substitutional and interstitial defects. Further, the differences due to Fe doping in pellet and thin film samples can ultimately be attributed to different surface to volume ratios.