I am working at a endless runner game with obstacles. One of my problems in this moment is that the box colliders on the obstacles works only when the element is on the middle line, if i move it right or left the box collider is not working anymore. If i resize the box collider to be bigger they work on the sides. (Imgur: The magic of the Internet)
Maybe your controller collider is not switching lanes? Visually the runner might move left and right, but try selecting the controller when the game is playing and see if its hitbox actually moves into the other lanes and intersects with the pylons.