Recent experimental findings have demonstrated that low doses of low energy helium ions can be used to tailor the structural and electronic properties of single crystal films. These initial studies have shown that changes to lattice expansion were proposed to be the direct result of chemical pressure originating predominantly from the implanted He applying chemical pressure at interstitial sites. However, the influence of possible secondary knock-on damage arising from the He atoms transferring energy to the lattice through nuclear-nuclear collision with the crystal lattice remains largely unaddressed. Here, we study SrRuO3 to provide a comprehensive examination of the impact of common defects on structural and electronic properties. We found that, while interstitial He can modify the properties, a dose significantly larger than those reported in experimental studies would be required. Our study suggests that true origin of the observed changes is from combination of secondary defects created during He implantation. Of particular importance, we observe that different defect types can generate greatly varied local electronic structures and that the formation energies and migration energy barriers vary by defect type. Thus, we may have identified a new method of selectively inducing controlled defect complexes into single crystal materials.