This is by far the most common problem that novice Flash game designers face. It's the result of two factors:
Not keeping the data that is used to make decisions in your game separated from the visuals on the stage
Not centralizing the code that updates the positions of objects on the stage
It's common for game designers to write code that checks where objects are on the stage, and then use that information to figure out where other objects should be. Instead, your code should first create an abstract model of the game, and that game model should tell the objects where on the stage they should go. This allows you to resolve ...