Chao Container #1
After the section where you have to do homing attacks on multiple electric sheield G.U.N. beetle robots over a large gap, you will see the Chao Container directly after it and before a checkpoint.
Chao Container #2
Directly after the above Chao Container, you will go through a large warp tube. You will exit upside down on the ceiling. Go to the end where you can flip the gravity switch, then turn around and there will be some springs to take you up on the platform (where you get the fire somersault power-up). If you keep going backwards you will see rails either side of the toxic green pit. Grind one of them accross the gap and it will take you to the second Chao Container.
Chao Container #3
After the part with a huge spiked balls rotating in the air, before a G.U.N. beetle robot guarding a locked door, there is a gravity switch and then a rocket that you use to break open a green protective barrier. The final Chao Container is inside there.