Some energy is used by organisms at each trophic level for their vital life processes such as cellular respiration and corresponding cellular functions which require ATP.
Some energy rich molecules are indigestible by consumers on the upper trophic levels because they lack the correct digestive enzymes. For example, humans are unable to digest many fibrous plants.
Absorption is never 100% efficient. There is always some material which has the potential to be digested but is not absorbed. It is excreted as waste.