More details are needed.
What version of MasterCAM?
What kind of CNC machine?
And if you can, give us the .MCX file and the posted gcode so we can look at it.
At a guess, you're using different tool planes to machine different sides of the part. This will normally generate rotary axis moves. But if the machine definition isn't set up for rotary axes, then you will get the warning that you saw, and the rotary code won't be posted.
I ran across a similar issue when I inadvertently commanded a 5 axis move on a 4 axis machine. See this thread for more details.