Most scenarios that have been mentioned here are "Runners screw up and brought it on themselves" and "Johnson misled them, to pay less".
They both happen, but usually Johnsons pay appropriate amounts of cash just to avoid bad rep and not getting any runners. Also they're interested in the mission being a success. If they offer 1k for a milk run, they'll usually not get pros, they'll get amateurs and beginners. If they know they're up against HRTs or the like, they know they just send 4 people in to die, with literally 0% of success. Unless you're the distraction for the real team that's just stupid. Better pay 20k per person, sure lot more expensive but suddenly the success rate is 98%.
There's a third option. "Johnson really figured it was a milk run, but something unexpected happens". Say the mission is to go to a hotel room in the barrens, and get a commlink and bring it back. Low security, expected to be back in 2 hours. 1k per person seems fair for an easy job. Now they grab the commlink and all hell breaks loose, as two gangs are taking shots at each other inside the hotel. Totally unrelated to the commlink or the mission, but if the runners aren't careful they're still dead all the same. The Johnson will most likely refuse to pay them more money, after all it wasn't his fault and those situations are exactly the reasons why you hire runners and not go yourself.
However: Not all the nuyen need to come from the Johnson after all. Say, beside the commlink they also found a snazzy cyberdeck, worth normally 200k. They can probably fence it for around 80k or so, which is another 20k per person. More than enough for a run of that difficulty. (Of course if they decide to keep it and give it to their decker, they get more money worth out of it, but less hard nuyen)
