So whenever I use "expand compound shape" (pathfinder selected button on the bottom left on that image) Illustrator adds those random dark corner to whatever shape I have. why?
Occasionally, after a complex Illustrator operation, my computer fails to update or "paint" the pixels correctly to my screen - and when I do a quick zoom-in / zoom-out, it refreshes and repaints the graphic correctly.
I assume you likely already ruled this out, but, worth mentioning.
I've had the same issue – sometimes I find it happens when I'm working on something at a very small scale. If I scale the object up substantially then perform the Pathfinder effect, it renders perfectly. Worth a shot.
Could you please upload an image of the actual paths? You can get the path view (onion) by pressing Cmd+Y (or Ctrl+Y in Windoze). That will help a lot to understand what's happening ;)
Also, have you tried just to convert strokes to outlines through "Flatten transparency"? I get some errors when I use expand with compound objects time to time, even though logic says it is the same (and the very same module used for expand), don't ask me why xD