The embedding is an essential step when calculating on the D-Wave machine. In this work, we show the hardness of the embedding problem for all types of currently existing hardware, represented by the Chimera and the derived Pegasus and Zephyr graphs, containing unavailable qubits. We construct certain broken Chimera graphs, where it is hard to find a Hamiltonian cycle. As the Hamiltonian cycle problem is a special case of the embedding problem, this proves the general complexity result for the Chimera graphs. By exploiting the subgraph relation between the Chimera and the derived graphs, the proof is then further extended to the Pegasus graphs and to the Zephyr graphs.