Players should be living with the fact that their characters are always outnumbered and always outgunned. Perhaps not in a given fight, but the other side, be it a corp, a criminal group, a government, what have you, has more guys, more resources, more time, more money than they do. Runners survive by keeping it anonymous and making it more trouble than it is worth to track them down and do them in.
A runner who doesn't have a thought in the back of his mind that if things go pear shaped they will be staring down 40 assault rifles with under barrel grenade launchers isn't seeing the bigger picture.
Sometimes intell is old, wrong, or flat fabricated. The guy who is willing to sell you the security specs might have a file that is five years old, might have something from another facility, or something he banged together with an edit program. Why did he do it. He wanted the money, honey.
Contacts have their own problems. Sometimes they don't know what you want to know, have been leaned on by someone bigger than you, or just flat got a better offer.
Sometimes your luck just flat blows. The day you pick for the extraction a senior V.P. is touring the facility and there are 30 extra guys in milspec armor with machine gun toting rotodrones on the perimeter.
Sometimes you get back to the meet with Mr. Johnson and he has decided its cheaper to kill you than pay you. He has 8 cybertrolls with Gatling guns waiting to take the package off your hands.
You aren't the only runners in the sprawl. There can be another team after the mcguffin. There can be anther team who has been hired to remove your liver through you left ear. Smart professionasl who know all the dirty tricks the player characters know are about the worst enemy there are.