This is reported speech, also known as indirect speech, and so has been back-shifted. If the person had been quoted, the line would perhaps have read:
I had seen the question in one of your articles, Mystery of Friendship.
When one talks about something that another person said (or wrote) in the past, without directly quoting that person, the tense of the reported verbs is shifted one degree farther into the past to indicate the time frame when the speech occurred.
Suppose that some time ago, John said "I am going to the store" to Martha, using the simple present. If Martha had later recounted this to Fred, she might have said:
John said that he was going to the store.
shifting the verb from "is" (simple present) to "was" (simple past).
If instead John said:
I was going to the store, but I've changed my mind
then Martha might report this as:
John said that he had been planning to go to the store, but didn't.
thus shifting "was" a step further back to "had been"
Depending on the situation, and the exact meaning the speaker wants to convey, back-shifting may be optional or required.
The original speaker would have used "I had seen" because this is an action in the past, now completed, so the past perfect is appropriate.
For more on back-shifting, see: