I have multiple libraries with the same movie in multiple libraries. For example, I have Star Wars in ‘HD Movies’ which is the Blu-ray version, and Star Wars in ‘VHS Movies’ that’s a VHS rip on my LG TV and Asus Nexus Player.
When I stop watching one of them and save it for later, my On Deck (and continue watching section on consoles/apps) has multiple Star Wars showing instead of one. This happens with any movie that has another version in another library (say a fan edit of Terminator 3 in fanedits, and Terminator 3 in HD Movies).