One of the commands Milo enters when accessing the surveillance system in the day-care center is "show -p 1984", this is a reference to George Orwell's book "1984" which describes a completely controlled society where everyone is monitored by the government.
NURV is shown to stand for "Never Underestimate Radical Vision" on a sign at the entrance to the campus. This is also seen on a whiteboard during Gary's first motivational meeting that Milo attends.
When Bob comes back to his office where Milo is waiting, Milo asks him if "everything was ok." When he says that, he puts is elbow on the arm of the chair, but when the camera shows him from a different angle, his arm is down and then he puts if back on the arm of the chair as if he had not done that before.
After Teddy is killed, Milo is handed a CD which contains new source code that solves the bandwidth limitations. Unless Gary refactored it considerably, Milo would be able to spot Teddy, and possibly his own coding style instantly. Combined with Gary's comment "its not in the box, its in the band", it makes no sense for Gary to hand Milo such condemning proof.