Usually it's a vehicle that detects a fault and stops (audio continues), causing the control system to "Ride Stop." In this case, the show effects stay on. During a ride stop, it is possible for the vehicle intervals to misalign (they stop at the end of the block zone they are in). So when a vehicle triggers a scene, and the one behind it is now too close, the scene doesn't have time to reset and you see a blank screen or miss out on certain effects. Once the ride restarts and all the vehicles are cycled, everything syncs up again.
The other thing I heard (from various TM's) was that depending on the severity of the fault, the vehicle will literally turn itself off, and cause the control system to auto E-Stop, which faults out all show effects and kills power to the track.
I can guarantee though, if your vehicle stops for more than one second, the TM in controls knows about it, and usually they will let unload know as well.