In my experience the GM doesn't need to do anything extraordinary to make things go FUBAR. All it really takes is there being a variable that the team didn't find out about or something, or a double cross is always possible. Just be sure to make it possible for them to figure it out first with legwork, that way if they don't it's on them for not doing their research (and be legit about it, don't make it impossible to find out).
A run gone wrong can be a ton of fun if done correctly. My players have been on the run from their employers now for a bit because the Johnson figured they knew too much and couldn't risk the potential liability, so he sent a corporate mop up team to the debrief instead of going himself. They got away and are now in a combination hiding/revenge mode that's gone on for at least eight sessions or so. I've been very harsh on them, but it's been realistic, a lot of fun for everyone, and if they can make a positive resolution on the situation I intend to reward them handsomely.
Another fun thing I did once, and that is start with things already gone FUBAR. Obviously this has to be talked out with your group first, but the basic idea is this: instead of giving them the job and letting them do legwork and everything, you tell them the job they already accepted, what they were able to find out, and how the run has gone so far. I know, it's railroading but that's why you discuss it with them first. Anyhow, they begin the story in the middle of the run, just as it hits the fan.
What I did on mine was this:
The job was a data exchange (street to lower corp level run). The Johnson is paying the group to buy a chip with unknown data from an individual for an already agreed on sum. The Johnson does not completely trust the seller and that is why he's hired you. The job is to find out in the next 12 hours if the seller has any history of betrayal and if not to exchange the J's cred for the data. It seems like a milk run with good pay, but not so much pay that it raises eyebrows.
The seller checked out. No major things stand out as a risk.
So the team goes to make the exchange in unused warehouse. As GM I place them where they would reasonably be (if the Hacker normally hacks from home/the van then he/she's home/the van, the Sam by the window watching, the Face talking to the seller, etc). They're about to make the deal when the Street Sam suddenly sees several LoneStar cars pull up and men deploy, taking positions around the building. There is an announcement that the building is surrounded and to surrender themselves.
The seller turns his back to the Face, pulls his pistol and holds it ready. "Drek! We've been set up! We gotta get the frag ou-" Just then, his head erupts into a spray of blood and bone bits. The Face just manages to see a pane of cloudy glass shatter and in the distance behind it a figure of a man in an all black bodysuit get up with a sniper rifle run across the rooftop of the next building and disappear.
The players got to take it from there.
Obviously there was much more to the story then that, but that was all things the players had to figure out to get to the bottom of things, after they managed to get away of course.
