Every human was born different. And as they grow through society, through the influences of everything around them, they begin to develop a set of preconceived notions, thought processes, biases, logic, etc.
Even though this streamlined their mind, it also meant that anything not belonging to these 'lines' fell through their mental grasp, leading to what was known as blind spots, things or ideas they glossed over naturally, having never pondered in such a direction or entertained such a train of thought.
As Compass Carburettor relied upon Pilkan's brain, the way thoughts were processed here was the method that Pilkan's brain was trained for through repeated practice over his entire life. And hence, the moment he became a Human Invoker, his train of thought led to him thinking that all enemies—humans—must be killed to harvest their Mental Fragments.