Chao Container #1
After the second checkpoint, you have to hover up some platforms. Some platforms have a big pyramid structure you need to shoot with your regular gun - the Chao Container is hidden inside one of these.
Chao Container #2
After the on-rails section through space, before the next checkpoint the Chao Container is hidden just under the ledge you need to jump down from.
Chao Container #3
After the part where you need to jump across a bunch of platforms and hover up them, you will get to a tall indoor shaft that you have to work your way up. Once at the top, you have to fall/hover down the other side, and the Chao Container will be at the bottom.