And not one single pilot ever testified to being told that "real life will be A".
You are joking. Right?
So when, the night before the flight, you see the contradiction, you have to sort it out, properly.
The whole point is that you cannot be expected to see any contradiction.
There were only four digits changed of some thousand or so digits on the flight plan. The standard waypoint entry check is to compare the flight plan data with the data in the navigation system. It is not to check the flight plan data with co-ordinates on a map.
The flight plan data matched the data in the aircraft's nav system, so the crew had done everything expected of them. The problem was that the final waypoint had been changed and the crew were not told about the change.
Do you start to get the idea? The company changed the flight plan that the crew were relying on, and did not tell them about the change.