Most likely the problem is the pen or the paper shifted.
If that’s not it, check the machine mechanically:
- Pulley set screws: http://docs.carbide3d.com/shapeoko-faq/shapeoko-3-how-to-check-the-pulley-set-screws/ — be sure to check all axes/pulleys including Z.
- V wheels / eccentric nuts: http://docs.carbide3d.com/support/tensioning-eccentrics
- Belt tension — the Z-axis should be guitar string tight (but careful not to bend the motor shaft): http://docs.carbide3d.com/assembly/shapeoko/xxl/step-5-belting/ on deep cuts it may help to remove one spring from the Z-axis temporarily, esp. if one hasn’t added a spoilboard on top of the wasteboard — it also helps to install the router as low as possible (installing the Makita adapter upside down will help). Some folks have found it helps to remove the M4 Z-axis tension bolt, apply a thin bead of threadlock along the length of the threads, then reinstalling it after it has dried. See the video at: https://www.youtube.com/watch?v=_lIIb_PdziA Note that the X-axis motor is held in place on standoffs and if those bolts are loose this can cause belt tension issues.
Beyond that it’s usually a matter of Calibration and Squaring the Machine c.f., http://docs.carbide3d.com/shapeoko-faq/how-to-calibrate-the-machine-for-belt-stretch/