So I attempted to use the auto-mill function. It did not mill anything, but in my faction deck building screen, it only showed 2, where prior it was showing 5 of Predatory Dive, I also did not receive any scraps. I closed and restarted the game at this point.
However, when I was in the no faction deck building screen, I noticed that the 5 Predatory Dive still remained. Then I went back to my monster deck building screen, it still showed 2, but when I right-clicked on the card, it showed the full value that I still had. Still no change at this point in my scrap credits.
I was able to scrap manually and receive scrap credits.
Long story short, it seems to be a bug in that it does not auto-mill at all but will show that it did in the faction deck building screen, but the cards in the full deck view were never milled and could be milled manually. A mix of auto-mill not working and a graphical bug.
Even though I scrapped 2 of the 5 and left 3, it still shows only 2 in the faction deck building screen.