Automated fault detection is an important part of a quality control system. It has the potential to increase the overall quality of monitored products and processes. The fault detection of automotive instrument cluster systems in computer-based manufacturing assembly lines is currently limited to simple boundary checking. The analysis of more complex nonlinear signals is performed manually by trained operators, whose knowledge is used to supervise quality checking and manual detection of faults. We present a novel approach for automated Fault Detection and Isolation (FDI) based on deep learning. The approach was tested on data generated by computer-based manufacturing systems equipped with local and remote sensing devices. The results show that the approach models the different spatial/temporal patterns found in the data. The approach can successfully diagnose and locate multiple classes of faults under real-time working conditions. The proposed method is shown to outperform other established FDI methods.