I'm afraid that people have the habit of interpreting their dogs body language as if the dog was a human.
The dog may know that it has done something wrong but it is not showing guilt. It is trying to appease you by showing submission in an effort to avoid punishment or dissaproval. Guilt implies that it is regretful or sorry for it's actions. It is simply trying to avoid puishment. An interesting point is that very often the dog will not actually remember the exact action that it thinks will bring punishment or dissaproval. It is likely that after the "naughty" deed a feeling of fear was experienced and it is that feeling the dog shows - not regret for what it has done.