Como que

A prolonged and incredulous ¿Quéééé? is perfect for when you heard what was said but you can't believe your ears. And if you want to be specific about the part you find outrageous, that's where ¿Cómo que ...? comes in.

• La cama no va. — ¿Cómo que no va? The bed stays. — What do mean the bed stays?! It goes.
• No puedo. — ¿Cómo que no puedes? I can't. — What do you mean you can't? Of course you can.
• ¿Qué hago? — ¿Cómo que qué haces? What should I do? — You're seriously asking what you should do? It's obvious and you know it.
• ¿Cómo? — ¿Cómo que cómo? How? — What do you mean: How?

As you can see from these examples, after cómo que you simply repeat the language in question, changing the grammatical person as necessary, for example, from puedo to puedes in the response.

Cómo que

¿Cómo que ...? can also work for when you heard what was said but you genuinely don't understand the overall meaning. ¿Cómo que en diez pirata? What do you mean by en diez pirata? I heard the words and I know what they mean individually but I don't understand the whole meaning of what you said. This could be useful to you when you want to ask, in the same way a native speaker might, about the meaning of a new expression.