There are a couple of things you can do.
First is to always check to make sure the cut is complete before you move the material on the bed, because that is one sure way to make sure the second cut lands in exactly the same place. Anything subsequent is going to be a little bit off. (As you discovered, so no secret there.)
Second thing is to run the Camera Recalibration tool, and use the Set Focus before you print on it. Set Focus is going to make adjustments for the camera fisheye distortion wherever it is clicked. So you’ll be able to get much better visual alignment at that spot. The Recalibrator will improve the visual alignment overall.