Have there been any incidents caused by an inability to shut down an engine? I read many items on the avherald.com site where it says "engine shut down during flight" or words to similar effect.

I'm wondering if there are any instances where an engine could not be shut down or the pilots had trouble shutting down the engine when commanded. What sort of backup systems are in place to avoid this kind of scenario?
Qantas Flight 32
Enroute to Sydney, Engine Number 2 of the A380 disintegrated explosively. The shrapnel of the explosion destroyed many systems, including a hydraulic system, the anti-lock braking system, flaps and electronic controls.
After emergency landing, the pilots were unable to stop engine number 1, because the controls had been destroyed by shrapnel. Emergency services had to douse the engine until flameout was achieved.

Source