The best explanation I have from what I experienced with the Rogue - Barrens challenge is that the challenges are coded to only trigger when the correct version of the correct cards are played.
In the case of the Rogue challenge, copying a decklist auto-used the Core version of Plagurise, which wouldn’t trigger the challenge. If you replaced it with the Scholomance version of Plagurise, the challenge would trigger.
I suspect the same thing has happened with the Hunter Challenge, where it was previously looking for the Core version of Snake Trap, but as of rotation, Snake Trap has been removed from Core and so only the Legacy version exists. However the Legacy version is not suitable to trigger the challenge.
It is very possible that the exact same issue is now causing the Nathria puzzle to not launch correctly, as certain checks require Core versions of the cards that no longer exist as of Rotation.