Autonomous systems, such as self-driving cars and drones, have made significant strides in recent years by leveraging visual inputs and machine learning for decision-making and control. Despite their impressive performance, these vision-based controllers can make erroneous predictions when faced with novel or out-of-distribution inputs. Such errors can cascade into catastrophic system failures and compromise system safety. In this work, we compute Neural Reachable Tubes, which act as parameterized approximations of Backward Reachable Tubes to stress-test the vision-based controllers and mine their failure modes. The identified failures are then used to enhance the system safety through both offline and online methods. The online approach involves training a classifier as a run-time failure monitor to detect closed-loop, system-level failures, subsequently triggering a fallback controller that robustly handles these detected failures to preserve system safety. For the offline approach, we improve the original controller via incremental training using a carefully augmented failure dataset, resulting in a more robust controller that is resistant to the known failure modes. In either approach, the system is safeguarded against shortcomings that transcend the vision-based controller and pertain to the closed-loop safety of the overall system. We validate the proposed approaches on an autonomous aircraft taxiing task that involves using a vision-based controller to guide the aircraft towards the centerline of the runway. Our results show the efficacy of the proposed algorithms in identifying and handling system-level failures, outperforming methods that rely on controller prediction error or uncertainty quantification for identifying system failures.