Maybe your grammar book gave a general rule that in questions you should use yet; however, we often use already in a question.
Sometimes already shows that you didn't expect something or that you are surprised:
a. You don't need to talk to him.
b. Why? Have you already spoken to him? (Here, you cannot use yet.)
Have you already finished? (I thought you would need more time.)
Have you finished yet? (I just want to know if you are finished.)
Student or Learner