Core-collapse supernovae are the first polluters of heavy elements in the galactic history. As such, it is important to study the nuclear compositions of their ejecta, and understand their dependence on the progenitor structure (e.g., mass, compactness, metallicity). Here, we present a detailed nucleosynthesis study based on two long-term, two-dimensional core-collapse supernova simulations of a 11.2 M$_{odot}$ and a 17.0 M$_{odot}$ star. We find that in both models nuclei well beyond the iron group (up to $Z approx 44$) can be produced, and discuss in detail also the nucleosynthesis of the p-nuclei $^{92,94}$Mo and $^{96,98}$Ru. While we observe the production of $^{92}$Mo and $^{94}$Mo in slightly neutron-rich conditions in both simulations, $^{96,98}$Ru can only be produced efficiently via the $ u$p-process. Furthermore, the production of Ru in the $ u$p-process heavily depends on the presence of very proton-rich material in the ejecta. This disentanglement of production mechanisms has interesting consequences when comparing to the abundance ratios between these isotopes in the solar system and in presolar grains.