First, verify the BitSetter position per:
https://my.carbide3d.com/docs/shapeoko-setup/
Second, review jogging around and setting zero per:
https://my.carbide3d.com/gswso/06/
the warning is an out-of-bounds error as noted at:
https://carbide3d.com/blog/carbide-motion-bounds-checking/
for the BitZero see:
If you continue to have difficulties, upload your .c2d file, step-by-step notes on how you are securing your stock and setting zero relative to it and managing all tool changes and a photo showing an attempt at cutting still in place on the machine with the machine at the origin or a specified offset from it.