Some recipes depend on the dough being mixed just until the ingredients are combined, and not any longer. Other commenters are saying that overmixing cookies can warm the butter too much. With some recipes, like muffins, mixing creates gluten chains that lead to chewey-ness and toughness. So in order to avoid that you stop mixing asap.
Baking is a chemical reaction and the quantities, order, and methods really do have a huge impact on the result!