I have this bug too. I play singleplayer and use Nitrogen. I read in another thread to us the "pois" command to make it go away. It works!! I do not know what that command actually does, when i use it it says pois disabled. But, I have not noticed anything unusual nor not working as it did before. The pois function exactly as they did before i used the command except no marble blocks everywhere. When you see the phantom blocks, open the console and type pois. Problem gone. I was ready to stop playing and wait for stable and now I can play again, try it.