I think if I didn't really know where the anomaly was, instead of guessing where the intersection zone is I would look at the clock waveform trigger that looks correct and draw the box somewhere to the right of the trigger where the clock signal is high and use the does not intersect setting. This way you capture any trace that doesn't follow the expected clock high signal. Very nice feature!
Good information, thanks. Could you have used the zone trigger and boxed where the signal should be and select "Not Intersect" to get the same result without having to guess right?