We share our findings and experiences when debugging an FPGA-based PCIe Non-Transparent Bridge (PCIe NTB) used in an Electronic Control Unit (ECU) for Autonomous Vehicles. After explaining key inner workings of PCIe and PCIe Non-Transparent Bridge we discuss debugging using embedded logic analyzers (Xilinx ChipScope / ILA), RTL Simulators (XSim from the Xilinx Vivado toolsuite as well as Questa Prime from Mentor Graphics) plus Visualizer, also from Mentor Graphics. We hope that you find this useful when you are preparing to debug your next FPGA project.