Why is the actual yield of ATP during aerobic respiration lower than the theoretical yield of 38 ATP molecules?

Although the theoretical yield can be up to 38 ATP molecules per molecule of glucose, this yield is very rarely achieved. It is important to consider at which stages the losses of ATP occur and why. Once 2 net molecules of ATP are produced after glycolysis, which occurs in the cytoplasm, pyruvate must be transported into the mitochondrial matrix, where the next stage will take place (i.e. the link reaction and the Kreb's cycle). Pyruvate is polar, so needs to be actively transported into the mitochondrion, so we initially lose some ATP to get the pyruvate inside the organelle. Some ATP is also used for active transport of reduced NAD+ produced during glycolysis into the inner mitochondrial membrane as for this we once again need an active transport mechanism. In the last stage of respiration, some protons leak through the inner mitochondrial membrane back inside the matrix, so proton motive force which spins the headpiece of ATP synthase to produce ATP is decreased, hence less ATP produced.