I opened a wild bundle today (2 legendaries + 25 packs), rightfully assuming that I'd at least open all of the rares + commons from Caverns of Time, seeing as I own all of the rares/commons from the applicable sets (Legacy -> Gadgetzan). Not only did I not get anywhere close to completing the new Caverns rares/commons, the majority of the cards opened were cards I already had 2 of in the old sets. Not previously disenchanted, not currently unowned - these were cards I already had complete sets of in my collection.
For example, I had 2x Jade Spirit from Gadgetzan, I opened 2x Jade Spirit with the CoT set logo, meaning I have 4x Jade Spirit in my collection without the 'disenchant your duplicates' option in the collection manager. I don't know if this info helps in your quest to resolve the duplicates issue, but it really doesn't seem like intended duplicate protection behaviour. Definitely a downer, I hope there's compensation for the early adopters here.