Well...they did run on completely different circles and in big schools you don't always notice everyone. They spend a lot of time in season three/four about the fact that you don't always notice everyone in their school or even in their class.
Not saying it's right...but it is how things usually go in high school.
At least, I think...I went to a rather small high school. Most people at least knew others by face. However, even I had classmates I knew very little about.
Oh well...Then again I didn't see the epicness of Leyton in season one. Loved them later on, but wasn't on the lovetrain in season 1, so I didn't really mind things like her not noticing him before.