I believe I have found the problem. I tried everything I possibly could to reproduce this bug with a full inventory: crafting while the inventory was full, breaking down stuff and salvaging in a full inventory and harvesting with a full inventory. The extra items drop out of the inventory as expected and you just have to pick them up again when you have enough room.
However, upon watching your latest youtube video I noticed something peculiar. You seem to have missed the scroll bar on the right side of the inventory and think that your inventory is full when it is only half full. Scroll down in the inventory by dragging the scroll bar or use the mouse scroll wheel. You should find your missing items in the 4 extra rows of inventory slots that you have :D