Domain boundaries (DBs) generated during the growth of cubic silicon carbide (3C-SiC) on (001) Si and their interaction with stacking faults (SFs) were studied in this work. Direct scanning transmission electron microscopy (STEM) images show DBs are inverted domain boundaries (IDBs). The atomic arrangement of this IDB is different from the expected boundaries described in the literature; nevertheless, it has a highly coherent nature. The IDBs propagate in a complex way through the crystal forming “complex-IDBs” that interact strongly with SFs. In particular, we observed that IDBs can terminate and generate SFs. The presence of disconnections in the IDB could be responsible for this behavior. Some models are discussed in order to explain the interconnections between IDBs and SFs. Moreover, an ab initio Monte Carlo simulation was performed in order to shed light on the kinetics of the SFs–IDB interaction. We found that SF generation can be driven by surface instability during the growth of the crystal and that SFs can be terminated by IDBs.