While testing bugs, using Furball mission, multiple times I had defeated all incoming missiles with low throttle and flares, and then after the alarm turned off, I will regularly die to another missile that causes no alarms.
To reproduce, fly straight until your own teams AI starts firing missiles, and climb the hill to the right where the 2 windmills are, missiles fired at you there can be defeated using above techniques, but there is almost always one missile that still hits after alarm turns off (suspected Radar missile)