First, check your Z-axis belt tension — needs to be guitar string tight.
Then, plumb and square the spindle: https://wiki.shapeoko.com/index.php/Calibration_and_Squaring_the_Machine#Squaring_the_Spindle
then tram the wasteboard: https://wiki.shapeoko.com/index.php/Calibration_and_Squaring_the_Machine#Tramming
then, if you’re slotting, instead cut as a pocket as low as you can: Adding geometry to cut as a pocket with a finishing pass
If you continue to have problems look into leaving a roughing clearance and making a finishing pass and consider climb vs. conventional cutting.