Here are some screenshots of the issue. First, the list of atlas sprites under Unity 5.5, for reference on their real proportions (e.g. notice how all icon_issue* sprites are strictly square):
Now, here is Unity 5.6 atlas after 48x48px icon_data_01.png was added to it (ignore a few more icons like icon_help being present, Unity 5.5 example just happened to have them trimmed):
Notice how icon_data_01 sprite was generated incorrectly (it is not square at all and has incorrect border) and how icon_issue* sprites started losing their square dimensions? Next, here is a screenshot after two more 48x48px sprites are added to the atlas in Unity 5.6 (icon_data_02 and icon_data_03):
Now distortion affects more than a dozen of sprites. I have no idea how to fix this and this corrupts any UI where widget sizes are driven by native sprite resolutions, so I had to revert all my atlases and UI prefabs and started using Unity 5.5. to update them. Judging from the severity of the bug being dependent on the number of new sprites, I'd wager a guess that atlas update misreads the borders and dimensions of sprites around areas where new sprites are packed in. Going to experiment with switching to non-native packer to see if this goes away.
