Duration cards from previous turns really need to be separated from the cards you play on the current turn. I once had 3 Caravans in play from the previous turn; I played a Caravan, then played a Scheme, but I couldn't topdeck one of the Caravans from the previous turn because it thought I had selected the Caravan I had played that turn.
I just ran into this problem today. I'm surprised it's still an issue. I hope it will be fixed soon.