Waypoints currently use the window object, which is the iframe in this case. I don’t consider this desired behavior and have an open issue in our bug tracker for this to work in line with your expectations.
A workaround would be to manually create a waypoint (using the waypoints library) in the parent context on the iframe itself, and then use the Hype JavaScript API to perform animations. Programming required unfortunately.
I’m actually surprised the waypoints library, which Hype uses, doesn’t account for this already.