Chao Container #1
The first Chao Container is right at the start of the stage! But you need the bazooka power up that lets you destroy steel boxes. Simply look to the right when you begin the stage, and destroy the steel boxes which are blocking the path to the Chao Container.
Chao Container #2
Not far from the first Chao Container, go through the first cage where the doors unlock when the enemies are destroyed, there will be a lift just outside of it. Use it and turn around and jump onto the roof. Jump over the small fence and the camera will shift round to show you the second Chao Container locked behind a gate. Destroy the enemies and the gate will unlock! Hover over to the Chao Container.
Chao Container #3
The final one is also not far away. Directly after the first checkpoint, you will get to a room of G.U.N. robots. The Chao Container is in the corner of this room.