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I recently took a series of photo's of the moon (all at eh same time with the same settings) and have tried to use the auto align function in Photoshop but it keeps tellimg me that the photo's aren't overlapped by at least 40%... This is not correct as I have cropped the photographs to ensure the moon is roughly in the same place on each layer. Am I doing something wrong?
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Without having seen your originals:
This is pattern recognition. The surrounding black sky is just an empty area without any patterns, so it doesn't count. That's why it's not just 40% of total area, but 40% solid overlap, in this case, the body of the moon.
You can get around it with a tight crop, then move the result back to the original.