This is going to sound a little silly, but I've run into this.
1) Make sure the Z-zero is set properly. There are a bunch of ways to do this. If you're high by a few thousandths...this is what happens.
2) Make sure the material is the thickness you think it is. Measure it with calipers. I was really surprised how much variation there is in "1/2 inch material"
3) Make sure you're DOC isn't out of control, or you can cause the z to skip steps on plunge. Looks like there is a lot of chatter in there, and some of the cuts don't look like they're holding Z very well.
Any of these can leave you a little high by the time you get to the bottom of the cut.