I found such a sentence:
We had not reached the station yet when it began to rain
And as I see the logic of English people, it's so:
The action of "not reaching" happened firstly and only then happened the action "it began to rain".
What if we will add the word "already" to the rain part to make a hint that it should be Perfect, too:
We had not reached the station yet when it had already begun to rain
Is it correct? It's a problem, because both parts have some word which hints at using "Past Perfect". For the first part of the sentence it's "yet" and for the latter one is "already". What to do? Which action happened firstly then if both of them are in Past Perfect? Paradox...