I thought somebody here could help me out with that or at least tell me if or when there will be an update to fix this bug.
She tried to use the crank handle on the valves to stop the water from flowing up to the well.
The crank handle then "hovered" over the valve like it's shown in the inventory but although you can't combine these 2 things the crank handle didn't go back to the inventory. It just stayed there.
Then she went out of the room, saved and reloaded.
After reloading the crank handle was gone. It wasn't at the original location nor was it at the valve or in the inventory
Since I couldn't find a solution anywhere she restarted from scratch and took a new save slot.