There are some pretty realistic shots of an SLBM (Submarine Launched Ballistic Missile) flight during the last part of the movie. Naturally, it is interlaced with the climatic fight scene between our hero and the really nasty-ass villain.
During the missile's flight, it ignites a second stage, which surprised me. I thought all ICBM's, and especially SLBM's were single stage rockets. I figured Hollywood just added that to have something to show. I mean a missile just gliding along isn't that interesting. Turns out I'm wrong. All current US and Russian SLBM's use three stages.
They did get the re-entry scene wrong. When these things re-enter the atmosphere they are hustling along at a pretty good clip, like several miles per second. At those speeds friction with the air is going to heat up the warhead until it is glowing bright red. No sign of any re-entry heating in the movie.
Another thing was how long the final pursuit and fight lasted. You know how these scenes go in movies, they seem to go on forever. You know the hero will prevail, but they keep you on the edge of your seat for what seems like forever. You're pretty sure that if this was real life, the bomb would have gone off hours ago, and all this fighting would be for naught. Not quite the case. Ballistic missile flight times are on the order of 30 minutes from ignition to detonation, so in this case the time frame was plausible.
Ethan (Tom Cruise) made the mistake of not finishing off the bad guy before attempting to abort the missile. If he had just concentrated on doing one thing at a time, the fight would have been over much sooner and he would have had plenty of time to deal with the missile. But then we wouldn't have been on the edge of our seats as long.
SLBM's owe their existence to MAD, the policy of Mutually Asssured Destruction. MAD is just that: mad, as in insane. I can see where you might want to maintain the capability of building and delivering nuclear weapons, but keeping a whole arsenal of the things primed and ready for launch at a moments notice is just asking for trouble. Yes, someone could launch an attack and destroy every large city in our country and do it without fear of immediate retaliation. But what would that gain them? And how long would it be before the survivors, however few there were, found a method for exacting revenge? And how would the rest of the world treat someone who had unleashed a nuclear holocaust on us? Sure, a few nut cases might celebrate, but most nations would wonder who was next on the agressor's list. Having a bunch of nuclear missiles on hand, primed and ready to go, is a bad, bad, bad idea. If we removed all of our nuclear weapons from front line deployment, other nations might follow our lead.
Update: It occured to me that final impact sequence was wrong as well. Anything going as fast as it should have been would only have been a momentary streak and it's impact in S.F. bay would have created an explosion of steam and a mini-Tsunami that would have rocked every boat in the bay, at the least.