2 Rubies (Square) - The mines. The first is stuck to the side of the apparatus at the centre of the main chamber. The second is on the wall of the left-hand rock tunnel leading towards the exit from the main chamber.
Chapter 3-2
1 Ruby (Square) - Execution ground. As you approach the oil field refinery, it is on the wall to the right.
Chapter 5-1
1 Ruby (Square) - Underground garden. On the rock face above you from your starting position.