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)
Revealing mistake: When Ethan uses the magnetic screwdriver to undo the screws holding the grille to the air-vent in the NOC list room, the spindle that is actually turning the screw is visible after it falls out.
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.