I'm having this same issue, only not in the Ghost Shooter tutorial, but in my own game. Everything's been running great until a few days ago when I was putting a new sprite into my game and after editing the image it looked exactly like the OP's screen shot.
The same thing happens to the layer thumbnails on the right hand side of my screen and the little animation frames in the image editor. Hopefully there's a solution to this problem kicking around!