This is not a bug. It's how the OS works to keep track of locations of the icons when you view the drive in finder and more.

I guess you can open terminal to use ls to see them at a low level but these should not be tampered with. https://www.google.com/search?q=how+to+use+ls+on+apple+os

I can't hold developer classes here, just write it sounds as if it's fine.