Ilogical issues with unity

This has been driving me crazy and I cant for the life of me figure it out.

I have a class called Waypoint. It has no functions, and simply has a List that has all of its connections to other Waypoints.

I have another class that handles mouse clicks and then uses these Waypoints to figure out a path.

Every single waypoint has at least 1 connection, yet when returning a Count, if it only has 1, it returns 0. All other numbers work fine.

And to make matters illogical and confusing, the Count returns correctly for the number 1 after I switch between to the Scene tab and then back to the Game tab.

The two relevant files can be found at http://www.PlusIntStudios.com.au/Files

No other files have access or even reference these two scripts. In the editor, I fill up the connection Lists myself before running the program. I can watch as it returns a 0 count while at the same time, I can check that the count is indeed not 0.

Spent the night screwing around with it and still nothing.

I click on a spot that has 1 connection and it returns 0. I switch tabs, switch back, click again in the exact same spot, and now it returns 1.