Pine tends to compress when cut, then spring back, leaving such marks.
One way to get a finish pass effect for a pocket is to calculate the depth per pass so that the initial passes are at some reasonable depth, then the last is a thin cut.
Another possibility is your spindle isn’t square — ways to address that:
- tram your wasteboard: Wasteboard Plans with threads
- square your machine and spindle — see: https://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine#Tramming