Because you can't see something.
All is a very big word, are you sure you looked everywhere? The Map should say 100% all 171 squares should say 100% in all 8 sub maps in addition to the main map.
http://forum.djartsgames.ca/?thread_id=1856
And your profile should probably say 102%, yes there is an error in that.
But there has never been an error in not getting the Map to 100%, every case has had people not seeing something somewhere, a whole square, or a whole area.

You should check your profile for the number of Puzzle Pieces and Monsters, that can instantly tell you about how much you have forgotten.