Visible crew/equipment: At the end, when Tom Cruise throws the knife at Dougray Scott's feet, there is a quick succession of shots consisting of the two in a fistfight. In one of the quick shots, as Tom Cruise is debating throwing the knife, then charges instead, there is a distinct black shape at the bottom right side of the screen that belongs to neither Cruise or Scott. The shoulder of a crewman who got a little too close, perhaps?
Visible crew/equipment: At one point in the scene where Tom Cruise is escaping with the antivirus, but before he gets on the motorcycle, he jumps and sort of flips and manages to shoot someone while upside down. When he lands, the ground ripples like a waterbed, revealing that it was some sort of pad to cushion his fall.
Visible crew/equipment: During the bike chase at the end of the film, a stunt man in full leathers and crash helmet can be seen on one of the bikes - none of the riders were wearing anything like that.