It's rare that I miss a scan stop point, but it does happen. The cause is usually (a) the part was not loaded in the the fixture properly, hence the actual coordinates for the stop point don't even exist, or (b) the part has been miscut, where again, the actual coordinates for the stop point don't exist. The foolproof solution here, is to take actual points where the scanning is starting and stopping - on each part. Then use these actual coordinates to control the scan. I've done this on small parts, or thin parts, where start and stop points are very close to each other.
Mark