First, the BitZero is used to set zero relative to a corner or a surface — it is the BitSetter which if enabled and configured will be used to measure the tool whenever Z-axis zero is set. See:
Some potential causes of overcutting on Z:
- wrong Z-axis configuration — if an HDZ is selected rather than a Z-Plus when a machine has the latter it will overtravel, and the more aggressive movement can cause lost steps
- lost steps on retract, either because it’s a rapid and aggressive tool geometry next to a wall wants to pull it in, or something mechanically interferes (a too-heavy vacuum hose is a frequent culprit, or a power cord which gets trapped in the mechanism)
- the tool pulling the carriage into the cut due to too aggressive feeds and speeds for the current tool/tool geometry
Usually this is caused by a mismatch between job setup:
https://carbide3d.com/hub/courses/create/job-setup/
and how origin is set relative to the stock:
https://carbide3d.com/hub/courses/running-shapeoko/movements-zeroing/
I find that opening the .c2d file up and drawing a box which matches the specified dimensions (draw up the cut in profile if need be) or moving the machine to the origin and then using a tape measure to measure out the dimension(s) in question will make clear where things aren’t lining up.
Note that we have a blog post on it:
https://carbide3d.com/blog/unexpected-z-axis-plunges/
If you still have trouble, please upload the .c2d file and let us know step-by-step how you are securing your stock and setting zero relative to it and managing all tool changes, and send a photo showing the stock still in place after this sort of overcutting problem and the machine at the zero position relative to it (or a specified offset from that position) and screengrabs showing what Carbide Motion shows for Position and Machine Position (click on either to toggle to the other) as well as overall photos of your setup.