Improving the efficiency and accuracy of energy calculations has been of significant and continued interest in the area of materials informatics, a field that applies machine learning techniques to computational materials data. Here, we present a heuristic quantum-classical algorithm to efficiently model and predict the energies of substitutionally disordered binary crystalline materials. Specifically, a quantum circuit that scales linearly in the number of lattice sites is designed and trained to predict the energies of quantum chemical simulations in an exponentially-scaling feature space. This circuit is trained by classical supervised-learning using data obtained from classically-computed quantum chemical simulations. As a part of the training process, we introduce a sub-routine that is able to detect and rectify anomalies in the input data. The algorithm is demonstrated on the complex layer-structured of Li-cobaltate system, a widely-used Li-ion battery cathode material component. Our results shows that the proposed quantum circuit model presents a suitable choice for modelling the energies obtained from such quantum mechanical systems. Furthermore, analysis of the anomalous data provides important insights into the thermodynamic properties of the systems studied.