As far as I know right now:
- There are no issues with duplicate protection; it's safe to open packs. You're getting duplicates because you already have all of the cards of that rarity, as is expected.
- There is an issue where if you have 2 of an old card and 1 of the new card, the 1 doesn't show up in collection manager. We're working on this now.
(Upvotes appreciated so more people see this)