Factual error: When Tom Cruise is going to defibrillate Keri Russell to disarm the bomb in her head, no defibrillator takes 30 seconds to charge to 150 joules. Most go to 360 joules and if they are not charged in 10 seconds the batteries are depleted enough that they won't charge at all.
Continuity mistake: In the scene in Berlin, the female member of the IMF team starts with no special glasses/goggles, then has them up on her head, then, just before the shooting begins, she puts them over her eyes, but later, while the shooting is still going on, they are back up on top of her head. Then they completely disappear.
Continuity mistake: During the bridge scene, soldiers approach the armoured vehicle to spray it with orange gel. As they approach, the vehicle has a triangular reflector on the rear side. In the shot five seconds later showing the orange gel being sprayed, the rear reflector is circular.
Continuity mistake: Towards the end of the film, after Tom has been electrocuted to destroy the bomb implanted into his skull, we see the female lead trying to restart his heart, each time they show his eyes, they are closed or open in different shots, and if they are closed, you can see his eyeball moving underneath the eyelid.