I gouged a 3D part with 2 different operations. The first was Z-Level Rough, with a corner radius end mill. I selected the entire part as the geometry and was taking .100 DOC. The top of the part was undercut on 1 angle about .03 deep. Then after scrapping that part because of the gouge, I switched to a Slice Planar, with a ball nose end mill, and it gouged the the same type of part but in a different location.

Is this the norm for BobCad, does it often void the model?

Can you post the file so we can look at it? Or show some screen shots of what you were doing.

It's hard to tell what the problem is with out more info.

One suggestion for you.

Stitch your model together before running the tool path on it.