Scenario: You have some round button with content that bleeds over the top edge in the png file. You add blank white area below the circle to make the image's actual center the middle of the circle.
Step 1 Import the sprite into an NGUI atlas. NGUI trims off the transparency and adds a padding entry so that it can correctly center it back
Step 2 Snap to the right size and then lock the aspect ratio by setting size based on height
Step 3 Make the sprite smaller then the original art size
Result: The padding amount remains fixed as the image scales down, causing your image to get off centered
Desired: A percentage of the padding should be used based on the image sized compared to original art size.