The problems I have seem in accidents involving auto-throttles on both Boeing and Airbus is the pilots inattention to what is going on with the aircraft as it responds to thrust differentials. This may have been compounded in some cases by over-reliance on the automatics.
I personally witnessed one event in flight where a crew member bumped the throttle on one engine which annunciated and disconnected the AT. This was followed by immediate corrective action and re-engagement of the auto-throttle. The only problem was that after silencing the aural the PNF that bumped the throttle now missed the re-engagement with a fat finger punch. Over a period of time (many minutes) the aircraft responded by losing speed as it tried to regain altitude. It was recovered by the PF when he recognized the change in attitude.