If you change a UI object’s size in the level editor, it’s click area will no longer match up to its sprite, and as well its position will be incorrectly displayed when you move it around in the level editor.
I don’t know if this happens in the game layer or not; it just happened to me in the UI layer.
(And speaking of the UI layer, here’s a quick request again that Labels be made object-specific instead of shared within an object type…)