Hi tumbling_leaves,
This is a situation that can occur for different reasons. If you're using a tapered ballnose for finishing, it won't be able to reach everywhere that a flat endmill or ballnose endmill can reach, due to the taper angle. That could be the situation you're experiencing here, and you should be able to tell by looking at the operations simulated in PixelCNC. The remedy is to include a draft angle, typically that's at least a few degrees larger than the taper of your cutter.
There can also be machine-specific issues that arise, such as the machine flexing while cutting, throwing off where the cutter is from where it's supposed to be, or losing steps while cutting (which is a problem that stepper motor machines have) where the motors can't go where they are trying to because material isn't being removed quickly enough but the controller itself just assumes the steppers are always where it tells them to go - causing your machine's origin to shift. If the simulation looks good then I would wager that you're losing steps by working the machine too hard - or feeding too fast for your spindle RPM and the cutter you're using. The way you can find out if you're losing steps is by moving the machine to a known position after a cut to see if it thinks it is where it should be.
If you're losing steps you can try dialing back your feed rate, or increasing your RPM, or use a 2.5D milling operation for hogging material out first instead of a 3D contouring operation.
Hope that helps. Let me know how she goes and have a good week! :]
- Charlie