Here are a couple of possible issues where a fillet is performed on a transformed extrusion.
First, when the cylindrical extrusion of a circular cone face is split and a fillet is applied to the end cylindrical section, if the fillet parameter is "equal" (due to round off it may not be identical), the fillet is applied only to the outer end of the cylinder.
This geometry can be constructed and stored in MATLAB workspace as "g1" using:
The second is an error, though quite expected and detected, is accompanied by a geomtool crash. It results from erroneously specifying a fillet parameter on a cylinder circular face that is greater than the cylinder radius.
Once the crash is dismissed, a proper error message is displayed:
This can be reproduced by running "Fillet_Issues.m", selecting "F1", and issuing the undo operation and then selecting the outer cylinder and executing the Fillet option with a parameter of "0.21".
I thought you might want to prevent the geomtool crash, if possible.