This is the way cloning is designed. The clones are determined by the order that Pega Robotics matches to the control - therefore the developer should not rely on the control to order the cloned controls based on what you see on the application. It is unreliable. 

Usually, I assign custom keys to the cloned controls when they are created based on a property or unique value that I can reference later. In other scenarios, it is best to loop through the clone collection and analyze the control to determine what logic needs to happen next.