The efficiency of nanocrystal (NC)-based devices is often limited by the presence of surface states that lead to localized energy levels in the bandgap. Yet, a complete understanding of the nature of these traps remains challenging. Although theoretical modeling has greatly improved our comprehension of the NC surface, several experimental studies suggest the existence of metal-based traps that have not yet been found with theoretical methods. Since there are indications that these metal-based traps form in the presence of excess electrons, the present work uses density functional theory (DFT) calculations to study the effects of charging II-VI semiconductor NCs with either full or imperfect surface passivation. It is found that charge injection can lead to trap-formation via two pathways: metal atom ejection from perfectly passivated NCs or metal-metal dimer-formation in imperfectly passivated NCs. Fully passivated CdTe NCs are observed to be stable up to a charge of two electrons. Further reduction leads to charge localization on a surface Cd atom and the formation of in-gap states. The effects of suboptimal passivation are probed by charging NCs where an X-type ligand is removed from the (100) plane. In this case, injection of even one electron leads to Cd-dimerization and trap-formation. Addition of an L-type amine ligand prevents this dimer-formation and is suggested to also prevent trapping of photoexcited electrons in charge neutral NCs. The results presented in this work are generalized to NCs of different sizes and other II-VI semiconductors. This has clear implications for n-doping II-VI semiconductor NCs without introducing surface traps due to metal ion reduction. The possible effect of these metal ion localized traps on the photoluminescence efficiency of neutral NCs is also discussed.