This is called Element Binding and is intentional. The idea is that while developing a script in the graph editor, you will constantly be updating and modifying your graph to function in the way that you like. While doing this, it would be pretty annoying if Dynamo created a brand new instance every time you updated your file. Typically once a graph is complete and being used for production, it’s run through Dynamo Player which does not use Element Binding (it’s just a whole new instance actually). There are also ways to avoid Element Binding with Python, which you can find here on the forums. All of this is better explained in the linked post by Jacob Small.
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