Note: I wanted to add some screenshots to this post, but didn't have the time. I don't think it's super important, but it would definitely help outline the potential issue with Linked Documents.
Linked Documents are a great feature of Kentico. They allow you to create a page that is essentially a shortcut to another page in the content tree. To create a linked document you simply create a new document, and you select "Linked Document" instead of selecting a document type. If you're not familiar with the functionality, check out the well-written docs.
While linked documents provide some great functionality they can also cause a duplication issue. If you're using a Repeater to select a path that contains both the original and the linked document, both will appear in the list!
Fixing this with a repeater is easy. Simply configure the repeater and check the box that says "Filter out duplicate documents"!
Piece of cake!
Other List Controls
But what about menu web parts like the CSS List Menu or Drop Down Menu? This is a little trickier since they don't have options to automatically filter out the linked documents. Instead we can do it using a simple SQL Where clause. If a document is a Linked Document, the "NodeLinkedNodeID" field in the CMS_Tree table will be the ID of the original Tree Node. So we can use this as the Where clause for the menu web part:
NodeLinkedNodeId IS NULL"
(Note: you don't need to put "WHERE" at the beginning of the where clause when configuring Kentico controls)
Another piece of cake!