If the killer went have Ma Petrelli, and it appeared to have no one there. How do we know that the killer is doing a physical manifestation that is tangible? It is possible, if you consider the entity worse than the Boogieman sees Molly, it is possible the killer is able to do remote ethereal manifestations to do killing. The entity could also have a form of psychic reality manipulation, along the lines of the Scarlett Witch:
http://www.marvel.com/universe/Scarlet_Witch
This would then explain Sylar and a bunch of other things.
The entity in killing Hiro's father made an image appear so that Hiro's father would know who it was.
If this is true, the the enemy faced this season is VERY dangerous, but appears only to be motivated by revenge against limited targets.
- Rich