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.
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.
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.
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 of the movie, when Ethan and Luther are sitting at the pub, just after the cheers/here's to you speech, Luther said "Hey, I'm flavour of the month" and brings his glass up to his lips for a drink. In a split second cut to a wide shot facing Luther his glass is on the table, and there are only two glasses on the table as established in a wide shot where Ethan says, "I'd better go catch my flight."
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: 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: In the scene where Jim, Claire and Ethan are in the baggage car of the train Claire takes the money off of Ethan, the money is not folded in any way. However, in the next shot where she passes the money to Jim it is suddenly folded conveniently to fit into Jim's pouch.
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)
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: When Claire finds Ethan disguised as Jim, he has his normal hands. However, in all previous scenes of him in disguise, he has fake hands as well, that are wrinkled like Jim's.
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)
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.