So my first CNC project the”Luban lock” cut though material after the pass at about the 90% complete mark and into the support board. I followed directions in the manual for first project no idea what happened! The project was included with software so I assumed the gcode was correct.
I’m not an Artisan user, and I did not do any of the Snapmaker examples, but that said, milling into the waste board is pretty standard. The name waste board is telling it: At some point you’ll trash it and replace it. And it is always a good idea to mill a little deeper than the material strength if you want to be 100% sure to cut through completely. So, sounds like everything is as designed 
If you do not want to “damage” your waste board, put something else between workpiece and waste board.