This has been an ongoing issue since the early stages of the first beta. I think it might be an equip issue since the sovereigns never have the duplicate items equipped. On one hand, its a bug, but on the other hand since you don't get any money or any remaining cities when the enemy surrenders, its a nice cash bonus when you sell off the duplicates.
However, one thing I would like fixed in 1.4 is when you are selling items in the shop, the selected item is highlighed with a glowing box around it so you know exactly what item you are selling. Too often in my haste I've accidently sold something that I didn't intend to sell. It would be great to have a 1 transaction undo button as well.