Incorrect: He asked had I finished my work.
Correct: He asked if I had finished my work.
Correct: He asked whether I had finished my work.

An indirect yes/no question is introduced by if or whether. Note the word order.

Incorrect: He asked that what are you doing.
Correct: He asked what I was doing.

Incorrect: He asked to John why your father is angry.
Correct: He asked John why his father was angry.

In an indirect question the subject comes before the verb.

Incorrect: He said that his father died last year.
Correct: He said that his father had died last year.

Incorrect: I did not see him because he went out before I arrived.
Correct: I did not see him because he had gone before I arrived.

Incorrect: He got angry before I said a word.
Correct: He got angry before I had said a word.

Incorrect: There I met a man who was my classmate 20 years ago.
Correct: There I met a man who had been my classmate 20 years ago.

These are examples of the common failure to use the past perfect tense when the time of one past tense verb is more past than that of another.

Incorrect: I will call you when dinner will be ready.
Correct: I will call you when dinner is ready.

When the verb in the main clause is in the future tense, the verb in the subordinate clause should be in the present, and not in the future.