I think anyone might not use like this. please correct a question.
let's assume that we have just run out of coffee which we bought last week, which is much earlier than expected.

How come a bottle of coffee which used to be fully filled with beans has been already empty?

Question

I think anyone might not use like this. please correct a question.
let's assume that we have just run out of coffee which we bought last week, which is much earlier than expected.

How come a bottle of coffee which used to be fully filled with beans has been already empty?

Answer

You could say:

"Where has all the coffee gone?" 
"Is the coffee gone already?"
"We're already out of coffee?"

Answer

How is it that a bottle of coffee, which was full of beans when we bought it last week, is now already empty??