This is by design. It is to help soften the edges of sprites, and ensure edges are blended the same way as transparency inside the image. See this image:
<img src="http://www.scirra.com/images/crop1pxborder.png" border="0" />
The left images are cropped with no border, and the right images are cropped with a 1px transparent border. The top image is a tiny 6x6 sprite scaled up large, and the bottom image is just an ordinary 32x32 sprite rotated slightly.
Notice with no border two problems occur:
- top image: transparency inside the image blends smoothly, but the edges are hard, which is inconsistent. With the 1px transparent border it is treated the same way over the whole image.
- bottom image: edges appear 'hard'. With a 1px transparent border the image has 'soft' edges which looks better quality, because it allows the edges to linear blend to transparency.
When cropping the origin, image points and collision poly are also offset by 1px so it should realistically have no impact on the behavior of the game.
Does this really cause any practical difficulties? I think it's a nice tweak to ensure the best quality display of graphics, especially on rotated sprites.