When Steve and Jerry are on the plane to France, the clock next to Jerry reads 7:10. However, in the next shot, during the same conversation, the clock reads 12:00.
Steve (Michael Douglas) goes to see Jerry in a lecture theatre, and Jerry refers to speaking to Steve on the phone, which was never seen.
A submarine never would be able to get into the Great Lakes undetected, as Lake St. Clair's deepest point is 27 feet. The conning tower would be exposed the entire way.
The stolen Soviet submarine could not have appeared in Lake Michigan unnoticed because it would have to pass through several locks on the St. Lawrence Seaway to get there.
It should have been obvious that the box was not full of money. If it were, it would be much too heavy to be lifted by only one man.
Steve and the girl change into different clothes and get a special souped-up vehicle from an unknown source. However, as Steve had worked for the CIA, he would have had many contacts that easily could have provided the vehicle.
Steve and a girl are seen outside a building when the FBI brings Jerry out. Although they get in front of the FBI convoy, it's unknown how they knew where the FBI was going.