Fragmentation operation on two surfaces

Hi, I am performing fragmentation operations on surfaces that should result in holes on the main outer surface. It is working alright for 61 cases but 3.

I have tried adjusting Geometry.ToleranceBoolean, but it did not help. But, sometimes the problem goes away by adjusting the radius of holes.

To cut a circular hole, I am first creating spheres and extracting the surfaces of them. After that, I am performing fragmentation operations between sphere surfaces and the main body surface.

May I know the possible sources of errors?

I really appreciate your help. Thanks.

Hari