Basically there is a difference here. In the beginning when the Buddha explains contemplation of the body, he is really only talking about being aware of movements, or being aware of parts of the body, like the earth elements, water elements and so on or the 32 parts - where you actually think of your head, your hair, your skin and so on. So the first part of mindfulness of the body is a big group, so it is really concerned more with the body itself, its movements and its parts.
When the Buddha talks about the Five Aggregates in the body section, it's more to do with the process, the body processes. Your eye contact, your ear contact, your nose contact, your tongue contact, your touch contact, that is more what he is talking about in the Five Aggregates, the contacts that you have. So we are not paying attention to your stomach, your heart or whatever, we are not worried about the arm movement, standing, walking or whatever, we are only concerned with its contacts, what is happening at that time. That is the difference there.