Okay. Let's have a go at it.
While we are waiting for Mum, let me show you the great pictures I took in Peru.The word "took" is not even a verb in that sentence. It is part of the noun phrase "the great pictures I took in Peru". (What kind of pictures are they? They are the citures I took in Peru.) It would be a verb in this sentence:
I took those pictures in Peru.In any case, we only use past perfect when talking about something that occurred before another specific event.
Let's look at the other one.
Jane: Have you seen Sam? It's already 8:00p.m. and he's usually on time.Jane is worried about Sam. He is late, which is not like him. She asks Ian if he knows anything. Ian replies that "they" have just called (very recently called) him and that they are on their way. (They should be arriving soon.) He adds that they will be late because they missed a bus. (They probably caught a later bus.)
Ian: No, but they just called me. They are on their way. They missed a bus, which is why they will be late.
Is that helpful?