When cutting this cross I am having the problems as seen in the photos.
It is interesting that the anomaly does not carry to the outside of the through cut.
There is an offset contour .15 in deep around the top edge.
It looks like this is only happening on one side of the cross. If that is the case is the offset slightly smaller on the other side? I expect part way through the cutout carve you lost a step on your Y axis causing the machine to think it was in a different place than it was front to back. I would check all the tensions on your belts and try again. Maybe slow the cut down a little too if the belts all seem to be the correct tension. You should also check the Connections at the stepper motors and make sure nothing is loose there. It may have lost a step right at the motor.