Why does the mitochondria make carbon dioxide during cellular respiration

Because the organelle undergoes process that converts biomolecules into a useful energy resource for cell activities that leaves the formation of carbon dioxide as an excess agent.
Mitochondrion is an important organelle in most living organisms because it is where biochemical processes of living organisms such as respiration takes place. The mitochondrion has a smooth outer membrane but a larger inner membrane. The inner membrane is about 70% protein and is very convoluted because that can even fit inside the outer membrane. Mitochondrion is the carrier of the Kreb's cycle in the matrix and it is responsible for the transfer of electron chain found in the cristae of the inner membrane.

In the presence of oxygen, one glucose molecule has the energy to make up to 38 ATP. The ATP production is determined by the following steps, (-2 ATP) glycolysis preparatory phase, (7-9 ATP) glycolysis pay-off phase, (5 ATP) oxidative decarboxylation of pyruvate and (20 ATP) Krebs cycle. One glucose which has 38 ATP hence was the summation of all the process mentioned that took place.  All these process take place under the cellular function of cellular respiration.