There is only one way you can cause the toolpath to hit the bottom, and that is if you set a greater Stock to Leave than half the cutter diameter. It is a known habit and the reason is that the the cutter will "plunge" through the top surface during the calculation of the tip position, it is simply a mathematical issue.
There are two ways around the problem. Either use a larger cutter when you generate the tool path, it doesn't matter if you double the size as it is a Z-level operation only. Or, you can create a toolpath with Stock to Leave set to zero and then move the path where you want it.
If the depth is important (like in projected depth on a non linear surface), you should instead project the curve on to the surface with Rhino project commands and make an offset curve. Then, you can use MadCam's Along Curve instead on the new curve.