The past perfect tense is used in several different ways.
One of the most common ones happens when there are
two past actions and one happened before the other: the
past perfect tense is used for the first (earlier) action.
Another common use is in indirect speech--when reported
statements and questions follow a main verb in a past tense.

A third use is for the past unreal forms of conditional
("if") sentences and for wishes about past events. In both
of these, past perfect tense is used to show something
unreal or hypothetical in past time. (The difference in tense
and time is a "signal" that the event is not real or that it
is hypothetical.)

Examples:
Past Unreal Conditionals

If I had had time, I would've helped you.
(I didn't help you because I didn't have time.)

If I hadn't had a flat tire, I wouldn't have been late.
(I was late because I had a flat tire.)

If she had studied more, she would've had a higher score.
(Her score wasn't as high as she wanted because she
didn't study enough.)

If he han't been broke, he would've bought dinner.
(He didn't buy dinner because he was broke.)

If they hadn't saved their money, they wouldn't have
been able to buy a house. (They were able to buy a house
because they saved their money.)

Examples:
Wishes About the Past

I wish (that) I had studied.
(I didn't study, and I'm sorry.)

They wish (that) they had saved their money.
(They didn't save their money, and they're sorry.)

She wishes (that) she had been able to talk to you.
(She wasn't able to talk to you, and she's sorry.)

He wishes (that) he hadn't drunk so much coffee.
(He drank too much coffee, and he's sorry.)

We wish (that) we had taken your advice.
(We didn't take your advice, and we're sorry.)

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Special Notes: