Shapeoko 5 Pro not cutting square - how to get perfect right angles / corners?

Rather than cut a contour, offset by endmill diameter plus 10% and cut as a pocket down to at least tab height — where possible avoid slotting and add geometry and cut as a pocket

and/or

and consider leaving a roughing clearance and taking a finishing pass.

Also, check in w/ the folks at support to see if one of your Y-axis homing switches needs to be adjusted.