I don't know what your "tooling marks" look like, so it is difficult to determine what the cause is.
I think, very often that many machine operators are not aware of or how to "tram" the spindle to be "perpendicular" in two directions to the table top. This condition will cause tooling marks in the bottom face of a pocket and be very difficult to "sand out".
Not knowing your issue, I cannot be sure, but this is a common issue.
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