This research presents a novel framework for automated fault detection in cyber-physical systems, with specific focus on large-scale vehicle networks. Agents in a network develop system identification models of themselves which are sent to a local or global authority. The authority excites the system models and generates a fixed-size vector for each one using an echo state network coupled with an autoencoder. The resultant vectors are grouped using standard clustering algorithms, with each group representing similar system model responses. A human expert labels each group once, so that any new group members can be can be associated with the group label. The largest group is assumed to be operating nominally, with all other groups representing a fault or off-nominal operation. We apply our framework to a detailed vehicle cooling system model to demonstrate its efficacy.