I think I experienced the same issue. Every time I duplicated a node that had connected 'area_enter' signals and I used default flags I would get the error described above. My fix was to use the duplicate function flags to prevent signal duplication then add the signal after the duplication event.
I have provided the reference for the duplicate function. http://docs.godotengine.org/en/stable/classes/class_node.html?highlight=duplicate#class-node-duplicate
Godot Version 2.1.3.stable.offical
Error Generating Code:
var selfDup = self.duplicate(true)
var selfDup = self.duplicate(true,6)