If you press Alt+Tab and go back to the desktop, then hit Alt+Tab again back to the game does this fix it? also does this happen in the menu?
It doesn't fix it no, and it takes a long time to alt tab back to the game, a good few minutes. And it doesn't happen in the menu either, pretty much everything is fine, except for that on the screen.
And what's the skull?
As HEXiT said, It's a marker.
skulls a marker for a bad guy.