The chocolate chip, which represents fossil fuels, leave a hole or spaces when extracted from the cookie. Much like when we take fossil fuel underground, there will be empty spaces underground left behind when the fossil fuels are extracted. In the case of coal mine, there are surface mines. Surface mines level off mountains to extract the coals within. It can cause change of landscapes.
In the cookie's case, it looked ugly without the chocolate chip. In the case of the environment, the surface of the mountains are stipped off and are no longer capable of sustaining life.