The OP specifically referred to the Rotax 912. This engine is stopped by switching both ignition switches off. It does not have a mixture control or idle cut off. With this engine it is a nonsense to briefly switch both ignition circuits off and then back on again to "check that both circuits are off". Why? Because stopping the engine with the switches means that you have automatically checked that the ignition is off. If one circuit was still live, the engine wouldn't stop!!
Yes this does happen. To stop the engine if the switches don't kill it you have to switch off the fuel and wait til the carbs empty, or you can put on full choke.