When exactly do you get this issue? The meaning of the issue is that when Magento puts all items, in this case categories, in a collection. Everytime it "receives" a category, it will check if there is already an item in the collection with the same ID. If there is, it will throw this error.
The reason why this happens is different for every Magento installation. Do you use any extensions in your webshop that might have impact on the categories?
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