You can give me an example that is not duplicated by telling me the FID_Origin value in the intersect result.
Here is my example:
The two features with FID_Origin values 773 and 774 in the intersected output, with the calculated area of 0.071622 ha, are duplicated. Do you see them?
If you double-click one of them in the table to zoom to it, and then click the Select Features tool and click a location inside the polygon, at the lower left corner of the ArcMap window you should see "Number of features selected: 2". You have to make sure that you delete only one, not both, in an edit session.