Yes, duplicates do show up, this is only when adding through the "Add Core XXX to My Flashcards" link in the core word page (using the "Create New Deck" link and selecting all words works fine (except the missing kana...)). It happens at least on core 100, 200, 600 and 900 (haven't tested the rest).
In the core 200 list it seems that only タコ, 暖かい and 涼しい appear once, the rest are doubled.
In the core 600 list, one translation for "jogging" is ジョギング, while the second is "Ik voel me misselijk." which (according to google) is the wrong translation to the wrong language...
Hope this helps.