Continuity mistake: During the Job 3:14 scene, Ethan places the Bible parallel to the laptop and the gun. In the close-up angle it always appears that way, but in wider angles the laptop is slightly slanted. (00:34:15)
Continuity mistake: As the firefighters are entering Langley they mention they need to shutdown the air conditioning. The guard states that the aircon is in sector 21 that has no alarm. Luther 'helps' by triggering the alarm in that sector. A while later when Kittridge is talking to his people in the ops room you can see that the alarm is active in the 3 sectors as the guard mentioned but now sector 21 is missing. (00:57:30)
Continuity mistake: When the "firemen" (Ethan Hunt, Claire Phelps, Luther Stickell and Franz Krieger) leave Langley, Claire is in a red coat and red dress. As we see all four drive off in a fire truck, Claire is in a fireman's costume. Firstly, when did she have the time to change and secondly, why change? (01:08:00 - 01:10:00)
Revealing mistake: When we see a close-up of a knife being pulled out of a man's stomach, it's obviously a prop knife where the blade goes into the handle, as we can see the end of the blade while it's being pulled out. (01:19:50)
Continuity mistake: When Gene is handed the watch in London, the way he holds it changes depending on the angle. (01:25:10)
Continuity mistake: At the end of the film, Ethan drops his mask. His hair looks flat and wet. At the next shot it's dry and up. (01:34:20)
Continuity mistake: At the end, Ethan is drinking a pint and leaves a little left in the glass. This little bit of drink then vanishes is subsequent shots. (01:40:30)
Factual error: The vents that Hunt and his sidekick crawl down at CIA Headquarters are standard galvanized steel box vents; they are very common in the building trade. Try walking or crawling down one - you'll make a noise like the sky is falling down. People will be able to hear you for miles. Every person in that building would know somebody crawling about in the vent system. (This error applies to dozens of films, not only this one).
Factual error: CIA headquarters in Langley has its own firefighting unit and never, ever calls for outside help. In fact it is official CIA policy that they would rather have a building and its contents burn to the ground than allow unauthorised access by firefighters they know nothing about.
Factual error: The train is a French TGV, these do not operate in the UK (not to date anyway) The Channel Tunnel passenger train is the Eurostar.
Factual error: When the helicopter blows up, the train stops dead in its tracks almost instantly. A high-speed train like the TGV needs more then two miles to come to a complete stop from its top speed, or at least from the speed it's traveling at. And a Little Bird attached to it wouldn't make the slightest bit of difference.
Factual error: Max@Job 3:14 is an illegal e-mail address.
Plot hole: In the air vent, we see a rat. Wouldn't rats in the vents set off the alarms on a regular basis, because the lasers were on the upper side of the vent?
Factual error: In the scene where the helicopter is being flown into the tunnel, sparks can be seen on the far tunnel wall, where the rotors have hit it. No helicopter can keep flying in a straight line after the rotors have collided with a solid object in this way.
Continuity mistake: Besides the fact that during the final action sequence it is impossible for two trains to occupy the same tunnel, how is it that the blades of the helicopter attached to the first train don't strike the second? Tight fit.
Continuity mistake: In the scene where Ethan is in the NOC list room Krieger starts to drop him and Ethan is hanging there for a little while. Suddenly some sweat starts to drip down his glasses and he catches the drop with his hand. If you look at how close he is to the floor this move would be impossible.
Factual error: When Ethan is lowered into the computer room at Langley, he is dropped and nearly lands on the pressure-sensitive floor. When an object moves through the air, it pushes the air in front of the object. As the floor sensors were set so high that a drop of water was sufficient to set an alarm off, the air displaced during Ethan's fall would have triggered them too.
Continuity mistake: The train is electric, supplied by overhead cables, which do not appear to be present at any time. If it was a Eurostar then it could use 3rd rail pick-up but it wouldn't be going so fast, but that's academic; its not a Eurostar and no 3rd rail is visible either.
Factual error: The Channel Tunnel tracks run through separate tunnels, one going to France, one going to Britain, so trains don't pass in the tunnel as they do in the film.
Continuity mistake: When Tom goes to the restaurant to meet with Henry Czerny, the plants in the aquarium are noticeably different after he goes inside.
Answer: Ethan never thought it was a mole hunt to trap Jim. He found out from Kittridge at the restaurant that it was a mole hunt, but Kittridge believes that Ethan is the mole (the money his parents mysteriously receive). At the station Ethan realises that Jim must be the mole since it is too convenient both he and his wife survived. However, the hunt to catch the mole was never directed at Jim - Kittridge never suspected him until at the end when he sees Jim alive.
swordfish
Actually had suspicions before Jim showed up. Ethan found the Bible that was stamped from the Drake Hotel. Where Jim had literally just come back from before the mission. It made no sense otherwise why that would be in Jim's possession.