A variety of methods and devices for controlling the operation of the intake and exhaust valves in an internal combustion engine during skip fire operation are described. In various embodiments, an exhaust valve monitor or other suitable mechanism is used to detect exhaust valve actuation faults. When an exhaust valve actuation fault is detected for a particular cylinder, the corresponding intake valve is deactivated (or not activated) in circumstances when it would otherwise be activated in order to prevent the intake valve from opening into a cylinder that contains high pressure combustion gases. The described approach is particularly beneficial when skip fire operation is combined with cylinder deactivation so that air is not pumped through the cylinders during the skipped working cycles.