ok and this is new for me. I went to the mountains and harvested a crate of copper, closed the crate. When i got back to the forge, I took the crate to the smelter, opened it and couldnt grab the ore. grabbed the box and it moved as if nothing were in it, leaving the ore in the pile as it was in the crate. still cant grab the ore. not sure if it helps but the ore did glitch through the lid when closed.
edit: put the box back over the ore, opened and closed the box and now i can grab the ore. Good luck, I love your game.