Essentially, what happens is that you run too large a DOC, and the end Mill pushes the wood. Then the wood springs back up, and now the bottom surface is at a different vertical location.
You can fix it by running a tool path like this.
Rough Pass. .25 EM 0.00" to .22" deep
Finish Pass .25 EM start at .22 finish at .25".
Essentially, you run a finish toolpath with a very shallow DOC, which will eliminate this problem. Unfortunately, the nature of wood is that it will move on you, versus steel or Aluminum.