That's because they decided that if you had the card, you don't get another copy of it and they just use whatever is in your collection. So in the instance of Judith, the deck takes one, you have one, so it just used yours to craft the deck. If it took 2 and you had 1, it would just craft 1 of them and even your collection out to 2.
It's a shady way for them to do this and is probably why they delayed handing the NPE decks out so they could make it so that it gave existing players as little as possible, but this is what happened.
That's because they decided that if you had the card, you don't get another copy of it and they just use whatever is in your collection. So in the instance of Judith, the deck takes one, you have one, so it just used yours to craft the deck. If it took 2 and you had 1, it would just craft 1 of them and even your collection out to 2.
It's a shady way for them to do this and is probably why they delayed handing the NPE decks out so they could make it so that it gave existing players as little as possible, but this is what happened.