The food we eat is digested by various enzymes in our body. Why the same enzyme does not breakdown everything we eat? What significance does this have for degradation of waste material?

Enzymes are specific in their action, specific enzymes are needed for breakdown of a particular substance. For example, pepsin is needed to breakdown proteins while lipase is needed to digest fats. Because enzymes are specific in their action many human made materials like plastics cannot be broken down by bacteria and other saprophytes. These materials will be acted upon by physical processes like heat and pressure but under the conditions found on the earth these materials persist for a long time.