Chao Container #1
In the area where you walk around in a circle until you climb up to the higher level to continue, the Chao Container is just to the left of when you first enter the room behind some boxes.
Chao Container #2
Straight on from the first Chao Container after you jump up to the higher level, you will see the next Chao Container straight ahead in the next section. Can’t miss it!
Chao Container #3
Just after the platform section in the outside area, you will get to a part with lots of hovering G.U.N. robots in the air. Once you clear them you will have to take a platform down - it will decend down once you step on it. You will go past a Golden Beetle robot (shoot it if you like!), and once you get to the bottom, spin the camera around and you will see the final Chao Container behind you.