It's used to express surprise, confusion, or disbelief at something someone has just said.
Here are some examples:
* "Comment ça, tu ne veux pas aller au cinéma?" (How come you don't want to go to the cinema?)
* "Comment ça, il a déjà fini ses devoirs?" (How is that, he already finished his homework?)
* "Comment ça, tu ne connais pas Paris?" (What do you mean, you don't know Paris?)
It's important to note that "comment ça" can sometimes be used in a more sarcastic or ironic tone.