kieranmillar is right, this is be design. This way IRL you don't need to remember which/how many of your Merchant Ships were for +cards instead of +$. If you see a Duration card next turn with Way of the Chameleon in the kingdom, you do what it says on the card.
There are unfortunately cases where you need to remember if you used a Way next turn. When Way of the Mouse sets aside a Duration card, this can get problematic.