"You've never developed software in a large company, have you?"
Sorry - I've developed software in a considerable number of large companies including in Aviation.
"No one past a first level manager has much clue how the code works. Not even the grunts writing the code understand all the implications of the code"
That may well be the case, but a couple of grunts don't take it upon themselves to carry out what is essentially fraud without it coming from higher up the food chain,.
"And I can totally imagine that upper management never thought about the implications of each group on each other."
Then they have no business being in upper management.