There will not be any G2 / G3 moves with a wrapped rotary file.
G2 /G3 moves are arc moves (segments of a circle) within a plane, (X,Y X,Z Y,Z on most machines)
The current plane that a CNC machine is operating in, is normally set on a G-code controlled machine by means of a G17, G18 G19 code.
The output of a circle or any other arc segment drawn in the X,Y plane, when wrapped around a cylinder, would not result in G2/G3 codes.
As others have mentioned, your problem looks to be a mechanical one.
Does the control or control software that runs your machine, have a toolpath preview?
If yes, do you see the problem on the control preview window?