Chamfer created in the wrong place in the feature list causes an undesirable result.
This behavior is design intended as chamfer is a "local" modification operator. To get the desired result, consider create features in different order.
NotesExample:
In this case, apply chamfer first, and then do holes and extrude.
1: Chamfer at the end of the Feature gives the wrong result.
Champfer at the position before all other features created the result is as expected.