I just had something strange occuring to me, twice in a few minutes, both involving the item "Root".

First I had some roots in my chest at home, and I came back with one more root. When I placed the one root via quick move into the chest, the stack of roots in my chest just went to amount 1, the root I just put there.

I then went back to the dungeon to get more roots for a recipe, had exactly 10 for the first bow recipe, and went to the smith to craft it. I also had found one Rune Tool which I intended to use for the upgraded Sword & Shield.
I crafted the Training Bow, which should have used up all 10 of my roots (the game told me I had 10/10 before). After crafting, I still had 9/10 roots. When I wanted to upgrade the Sword & Shield, my Rune Tool was missing. The game somehow used the wrong ingredients for the Bow, it seems.

I don't know if bug #2 is related to bug #1, so I'm posting both together.