I forget the details of the episode, but did sylar actually see claire? Or did he assume that the other cheerleader was her the whole time? If so, Claire could have ran away. Possibly, the only reason Sylar knew that Claire was there was because Peter showed up, and pointed her out.
Again, I don't know the details, just trying to make up a reason in my mind.
I remember watching something on Stan Lee and Spiderman once, and he was getting grief for spiderman being able to sling his web from one part of NY to the Statue of Liberty. There wasn't any buildings for him to swing on to! How could he do it?! So Stan's response was, "...at that very moment, a helicopter appeared and he sung on that."
There are some things that we're going to have to chalk up to "TV Magic"...