Continuity mistake: When Travolta and Jackman are chased by the vans, there is a shot from Travolta standing in the car with a gun in his hands. A split second later there is a shot from the front, showing them sitting next to each other in the car. There's no way he could have gotten down so fast.
Continuity mistake: When the government agents try to take out John Travolta and Hugh Jackman, all of the SUV's are supposed to be Lincoln Navigators. Travolta destroys the first two. The third SUV turns left around a corner and it's a Ford Expedition, not a Lincoln Navigator. The scene cuts away and when the SUV is closer it's a Lincoln Navigator.
Answer: He wants to dupe everyone who investigates the problem into thinking it was an internal error, rather than a virus. Doing so would lead them away from Stan, and he would get away with the attack.
Ryan Andersen