1. A method of operation in a machine vision system operating in a run state, said method comprising: obtaining a pair of images comprising a current frame, from first and second cameras comprising a stereo camera pair, said stereo camera pair imaging a scene containing one or more reference markers; estimating mechanical misalignments in and/or between the first and second cameras, based on comparing current reference marker positions to original reference marker positions, wherein the current reference marker positions are determined from the current frame and the original reference marker positions are known from setup data stored in the machine vision system; calculating a worst-case error for stereo vision processing by the machine vision system, as a function of the estimated mechanical misalignments; and transitioning the machine vision system from the run state of operation to a fault state of operation, in response to determining that the worst-case error exceeds a defined threshold.