Entanglement is a crucial resource for quantum information processing. Protocols to generate high fidelity entangled states on various hardware platforms are in demand. While spin chains have been extensively studied to generate entanglement, graph structures also have such potential. However, only a few classes of graphs have been explored for this specific task. In this paper, we apply a particular coupling scheme involving two different coupling strengths to a graph of two interconnected 2-dimensional hypercubes of P3 such that it effectively contains three defects. We show how this structure allows generation of a Bell state whose fidelity depends on the chosen coupling ratio. We apply partitioned graph theory in order to reduce the dimension of the graph and show that, using a reduced graph or a reduced chain, we can still simulate the same protocol with identical dynamics. We investigate how fabrication errors affect the entanglement generation protocol and how the different equivalent structures are affected, finding that for some specific coupling ratios these are extremely robust.