What is this manga that has a guy with the power to make a transparent round bubble? I read it more than a year ago. 

A guy first has the power to make a transparent round bubble like thing and everything that goes in it or touches it disappears. As the story goes on he can make a bigger bubble.  

Then something shows up in the middle of his forehead - I think it was a third eye.  

I don't know if I am mixing two manga together or not but I think later on the more power he uses he turns into an ET (alien) looking guy.
The manga you're looking for is named Tanabata no Kumi. You're not mixing any mangas together, all what you've said is in that one.

Here is the synopsis:


  Basically, some humans have the ability to negate a sphere of reality, neatly removing it from existence. This gradually alters their appearance until they become a hideous alien, with a giant eye in their forehead.