Having this failure in such a trivial use case is really surprising.
Can you redo the screen shoot where we see the duplicate documents but make sure we see the same first line as the screenshot of the indexes? The first screenshot cuts out the long path of the database and collection name. And since you have complicated names.
My linux Compass is a bit old and I am not sure from your screenshot if the database is API and the collection is Insights.Dashboard.Traffic or the database is API.Insights and the collection is Dashboard.Traffic, …