Fully inorganic or metallic nanocomposite coatings are promising materials for various applications but face limitations in term of their synthesis. A complementary synthesis process, Physical Vapor Deposition combined with magnetron sputtering and plasma-assisted gas-phase aggregation produced Cu nanoparticles embedded in metallic matrix. In this study, the effect of embedded nanoparticles on the matrix structure was investigated. Al and Ni were selected as matrix materials due to their different sputter yields leading to different growth modes film morphologies and difference in surface energy. Depending on the nanocomposite and deposition conditions, defects such as nodular growth were occasionally observed. These growth anomalies originated from the presence of nanoparticles creating new nucleation points for the matrix to grow disturbing the grain growth around it. Key factors responsible for their formation include the surface energy difference between the NPs and the matrix and the geometrical disruption occurring for large NP. In extreme cases with a high concentration of nanoparticles, coatings entirely constituted of nodular defects were produced which can be advantageous for applications needing large specific surface area.