So pressing J to pick up items was often unresponsive meaning it was difficult to rearrange items to make the puzzle aspect fun. Moving left or right while on an item would sometimes pick it up instead of moving on the grid left or right. Pressing K would also only rotate the item occasionally as well. I did actually "bug" the game once putting a dagger on top of a bat, but after picking one of them up by moving the cursor left, I had to place it in a location it would let me place it.
I really don't know how to explain it better then that, and if that's just the inventory being hard to understand.... I highly recommend you change the way it works then, because it is very annoying an unintuitive for the player.