There are many unusual phrase that we use in England during our normal conversation and when I'm talking to friends in America they often stop me to question what I said.
This is a picture of some crows in a tree behind my home and the phrase of "Stone the Crows" is an expression of surprise like, "Stone the crows is it nearly 5 o'clock already". Looking into where this comes from I did like this answer. In the old sailing ship days when men stood in the crows nest on top of the masts for look out, they sometime fell asleep. A small pile of stones were kept on deck to be thrown at the crows nest to wake them up. The captain would shout a command "Stone the Crows".
My English phrases nearly got me into trouble when I was working in Arkansas, during a cigarette break with some of the workmen outside, I had run out of cigarettes and said, "Can I bum a fag". They all stood back and said you want to do what? My actual meaning was, "Can I borrow a cigarette", mind you they did give me a wide birth from then on.
Giggling so much at your story I can hardly write. We have all these sayings too brought to Australia by our grandparents. Yes a murder of crows indeed. Now you'll have to research the origin of that collective.