Quantum annealing solves combinatorial optimization problems by finding the energetic ground states of an embedded Hamiltonian. However, quantum annealing dynamics under the embedded Hamiltonian may violate the principles of adiabatic evolution and generate excitations that correspond to errors in the computed solution. Here we empirically benchmark the probability of chain breaks and identify sweet spots for solving a suite of embedded Hamiltonians. We further correlate the physical location of chain breaks in the quantum annealing hardware with the underlying embedding technique and use these localized rates in a tailored post-processing strategies. Our results demonstrate how to use characterization of the quantum annealing hardware to tune the embedded Hamiltonian and remove computational errors.