I have noticed for quite a while that while in layout mode, certain combinations of moving layout objects around will cause a single 'Undo' command to revert multiple moves. It is usually just the last two items, but I swear that I have seen it Undo more than two-steps back.
I think that it's limited to moves/repositions of layout objects - I don't recall if I have seen it undo formatting changes on multiple objects.
I have reproduced this in new empty files.
OS X 10.11.6
Create a new layout (Theme = Enlightened)
In Layout mode:
add a text object, a button, and a shape
Drag the text object to a new location
Click on the button to select it, then use the arrow keys to reposition it
Press "cmd+z" to Undo
RESULT: Both the text and the Button will move back to their starting positions, when only the button should move back.