Cut Simulation tool in fusion 360

Using f360, after selecting the lines to be cut, when i run the simulation, somehow the smaller, inner geometry (circles) are not included in the simulation. Why would that be?

A combination of your parameters in the 2d profile, parameters of your tool and the size of the geometry is discarding some contours.

Reducing or eliminating the:

Lead in Radius
Lead in length
Lead out Length
Pierce Clearance

Or/and adjust the Lead in angle.

Reduce the Kerf Width in the tool parameters.

Or/and Adjust the geometry of your design.

One or all of these may give you a solution and Fusion will be able to generate a path for all your contours.