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I am reading a story nowadays and I have noticed this sentence today the writer used past perfect and as I learned it should be in past simple because he/she gave the time yesterday.
The sentence:
I had missed school yesterday because of a doctor's appointment so of course I had no idea what had happened.
All verb tenses can be valid, when used appropriately.
Past perfect describes a past tense which occurred before another past tense, and that's useful when telling a story that's already set in the past.
"Yesterday" is in the past. So it's not disqualified from using past perfect.
If the narrator is telling a story set mainly in the present tense, the simple past would be better.
If the narrator is telling a story, where (even briefly) they are setting the point of narration to be in the past, and need to mention things which had occurred even earlier, then past perfect makes sense.
The sentence you provided, in isolation, is not enough to verify which tense is preferable, but there's a good possibility it's ok.
There is no rule that the past perfect cannot be used in a clause containing a definitive marker of time.
The outbreak of general war in 1914 had been preceded by the threat of war in 1911 and by local wars in 1912 and 1913.
So your concern about the time marker is misplaced.
The specific sentence that you asked about lacks any context so it is impossible to say whether the past perfect fits the sense or not. If, for example, the general context is about something that happened earlier today at school AND the past tense is being used to describe the events of earlier today, then yesterday preceded the general past of the story, and associating the time marker "yesterday" with the past perfect is appropriate.
