You haven't provided "simple_window.h" or "graph.h", so anything is a guess.
Since the compiler is saying that class Rectangle (check your spelling) is ambiguous, that implies there are two classes with the name Rectangle, presumably one in "simple_window.h" and one in "graph.h".
By qualifying the class name with Graph_lib:: you have specified which one of the two to use, thereby removing the ambiguity.
BTW, the using wasn't ignored. It just brought Graph_lib into the global namespace.
What AbstractionAnon is saying, is that by declaring using namespace Graph_lib, "Graph_lib::Rectanlge" is now "Rectanlge" and it is conflicting with another class called "Rectanlge" somewhere in your #include chain.
Also, did you mean "Rectangle" instead of "Rectanlge"?