The occasional plot twist I throw in my missions mostly relies on the team not getting the information about Johnsons' true motivations, which would come up during the mission, but not derail it. Or, some info provided is outdated or not disclosed. The tension and obstacles here are not created by the runners being deliberately shafted, and the plot twists serve not to throw extra drek at the players, but to enhance and deepen the plot. In fact, basing the whole mission on just the plot twist alone, IMHO, would be bad form.
Example: Assassination job, team is hired by a spook to take out a "retired" operative. Johnson provides info on target's whereabouts, and straightforwardly warns the team that their target is a trained professional. If they are not careful enough, they'll have to hunt down an ex-military sniper in a mountainous, forested terrain. Johnson insists that they take a biometric reading with a "black box" device he provides to confirm the kill. If pressed for motivations, the Johnson simply says that the target "knew too much", and that he does not want to risk his own personnel on this.
Plot twist: Some of the info that the Johnson has is lacking or outdated (e.g., the color of the target's truck is given wrong, and target's residence is off the grid and hard to find), leading to a few dead ends and false leads. This gives the target advance warning and time to prepare - and he is as dangerous as the Johnson let them know. The black box, if checked, is exactly what Johnson claimed it was, but the target is an HMHVV carrier, and coming into close contact with him, which is required to take the readings, risks infection.
So the plot twist here is, in fact, that things are exactly as straightforward as the Johnson put them! He may not have been telling them _everything_, or even right about some of it, but any omissions and mistakes did not affect the mission to the team's detriment.
I guess my favorite type of plot twists is The Reveal, where the motivations of the parties involved are explained and mistaken beliefs are shown as such.
Example 2: This is from a Scion game I've been running, based on Norse myth. The band of Scions (children of Norse gods) are contacted by Odin, and informed that the Aesir located where Loki had been building the Naglfar - a shipyard in Helsinki that he owns (those familiar with the mythos may appreciate the pun). Once they manage to sneak into the base and hijack the high-tech nuclear-powered aircraft carrier (in my game, one of the characters bribed a Scion of Braggi to stage a metal concert as a distraction, while the other two did a SR-style insertion by ultralight), and signal the scuttling crew to come in, Loki makes his appearance and reveals what his plan was all along. The ship in question was an attempt to aid the Aesir by cheating Fate - the legend says that Loki would sail the Naglfar with an army of dead to attack Asgard at Ragnarok. So here, he would use something that the Aesir actually have a chance of destroying, instead of the unstoppable monstrosity that is the Naglfar of legend. At the same time, the scuttle team arrives, and insists that the party finishes the job.
Again, the mission is as straightforward as it was given to the players. The ship is Naglfar, and it will be used against the gods. So the plot twist here actually comes after the party had pretty much already won. Except now they have a choice: finish the mission, or take a chance that the God of Lies is speaking the truth for a change and side with him, or walk away and let the two sides duke it out (which my party did).
