I just had this error myself and the answer from *hardwire* fixes the problem. Personally, though, I wanted to find out why and answer OP's question.
Simple answer. Handles.BeginGUI(Rect rect) calls GUILayout.BeginArea(Rect rect) underneath. But, Handles.EndGUI() does not call GUILayout.EndArea(). Therefore, the begins and ends don't actually match even when they do in your own code.
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