I can only find two Chao Containers in this stage…
Chao Container #1
After the indoor section with lots of urns and doors you have to break through, you will exit into an open space with G.U.N. robots firing at you. You can see the Chao Container past them and to the right. Destroy the enemies and when you are in the square space ahead of them, break the door and block to the right and you can get to the box.
Chao Container #2
There are two routes to this one. There is a part before the second checkpoint where you can take the lower route, shooting through steel boxes, or the upper route defeating some badniks. The lower route is where you pick up the Mystic Melody, which you then use to go through the mysterious door right to the Chao Container. If you take the upper path, you will see the second checkpoint ahead of you over the gap - but if you fall down the gap you will land next to the Chao Container.