Recently, remarkable successes have been achieved in the quality assurance of automotive software systems (ASSs) through the utilization of real-time hardware-in-the-loop (HIL) simulation. Based on the HIL platform, safe, flexible and reliable realistic simulation during the system development process can be enabled. However, notwithstanding the test automation capability, large amounts of recordings data are generated as a result of HIL test executions. Expert knowledge-based approaches to analyze the generated recordings, with the aim of detecting and identifying the faults, are costly in terms of time, effort and difficulty. Therefore, in this study, a novel deep learning-based methodology is proposed so that the faults of automotive sensor signals can be efficiently and automatically detected and identified without human intervention. Concretely, a hybrid GRU-based denoising autoencoder (GRU-based DAE) model with the k-means algorithm is developed for the fault-detection and clustering problem in sequential data. By doing so, based on the real-time historical data, not only individual faults but also unknown simultaneous faults under noisy conditions can be accurately detected and clustered. The applicability and advantages of the proposed method for the HIL testing process are demonstrated by two automotive case studies. To be specific, a high-fidelity gasoline engine and vehicle dynamic system along with an entire vehicle model are considered to verify the performance of the proposed model. The superiority of the proposed architecture compared to other autoencoder variants is presented in the results in terms of reconstruction error under several noise levels. The validation results indicate that the proposed model can perform high detection and clustering accuracy of unknown faults compared to stand-alone techniques.