This happens -in most cases- when a collision is found (direct collision with tool or with clearance around tool (e.g. holder clearance)
When I regenerate your operation (note that your part file as attached doesn't contain geometry) then all 4 holes go identical (as -without geometry-no collision will be detected for 1 & 4)
Off course you could switch off the collision check for non cutting but this check is there to get your attention. Something might be wrong. Maybe it is just the holder safety clearance that can be reduced for your application but maybe it is a real problem.
Without complete data including the part geometry file I will need to guess if part or check geometry is defined in the neighbourhood of holes 1&4 that cause a reject of the retract to the top of the hole (and instead execute a backup move to the clearance plane above).