To reproduce:
1. Open project "New Unity Project 1"
2. Select Main Camera
3. Toggle the button on the top left corner of the scene view
4. Notice how console starts getting spammed with "GUI Error: You are pushing more GUIClips than you are popping. Make sure they are balanced)"
5. Inspect the script TransformEditor - the only thing that gets disabled is the GUILayout.EndArea() call, this should not be a problem.

This seems to happen only when Handles.BeginGUI(rect) gets called. A more thorough explanation is given by a user here: http://answers.unity3d.com/questions/61190/gui-error-you-are-pushing-more-guiclips-than-you-a.html?sort=oldest