Why does my honda civic hybrid sometimes go into auto shut down at lights and sometimes it doesnt?
Because it saves on gas and electric. When a hybrid is stopped a light or tracks, the car charges. It it completely normal, and it is totally quiet when it is stopped
It is using the engine to run the alternator or some other charger (depends on the car but it is usually a more heavy duty charger) to charge the battery pack. If the batteries were to run out, it couldn't run the Honda electric assist until they are charged back up. It will normally shut off at a light to save fuel when it can but if the batteries are low enough on juice, charging is a stronger priority and the engine will stay on. Your vehicle is very high tech. All of the systems are monitored (things like state of charge of the batteries) and decisions are made on the fly by very smart computer controls, probably CAN or something similar. This is what decides to shut your car off or keep it running every time you pull up to a light.
