Attached, please find a zip file with 4 brep files.
I used BRepFilletAPI_MakeFillet to create the fillet on small.brep with radius=0.002. It results in small2.brep. The same step is applied to another part (big.brep) with radius=0.2. and it results in big2.brep. big.brep is 100 times bigger than small.brep. However, the results are different. small2.brep has 14 edges and big2.brep has only 8 edges.