Mission: Impossible (film)/Headscratchers

Mission: Impossible 2

 * The fact that a Welshman seems to be in charge of the American IMF is puzzling!
 * In the series they employ French, Australian, Scottish and English agents, likely amongst others- its not that surprising.
 * One thing that's not altogether clear is why McCloy goes along with Ambrose's plan. Grabbing the Belleraphon from Nakovitch is one thing given that he ran off with it, but having no problem breaking into his building and stealing the Chimera virus in order to sell it back to him? Why the hell would he go along with that? Did his company not bother telling him that armed men attacked his building, killed scores of guards and stole a WMD?
 * Whether McCloy was upset that Ambrose broke in and stole the virus doesn't matter once it was done. Ambrose has both the virus and the cure, neither of which McCloy wants being sold to anyone else.
 * Except that he offered Ambrose £37 million before that.
 * About the only possible explanation is that McCloy thought that Ambrose stole both of them from Nakovitch and not just Belleraphon, which Ambrose indeed had thought he had done at the start of the film. This doesn't explain why McCloy doesn't seem interested in or aware that someone stole another sample of the virus and slaughtered countless guards in the process, but evidently if he is concerned and aware he doesn't connect the dots and realize that Ambrose never had the virus in the first place and, thus, was the culprit of the attack on his company.

Mission: Impossible 3

 * Why is Ethan Hunt's wife allowed in the middle of IMF's headquarters at the end of the film? The organization is so secret, that they operate from the basement of a front business! That's a huge security risk they are taking for what is essentially a feelgood gesture. Imagine a real-world parallel: the wife of a high-ranking Pentagon official is kidnapped in order to get at her husband, and then she is rescued. I am quite certain the people at Pentagon wouldn't go, "Sorry we caused you so much trouble! To make up for it, come mingle with your husband's co-workers in a restricted area!"
 * Why does Davian torture Ethan, asking him where the Rabbit's Foot is? Ethan had it when he was drugged in a limo, and Davian's henchman should find and give it to his boss.

Mission: Impossible - Ghost Protocol

 * It's never explained how Cobalt hacked into IMF's communications during the previous mission or even knew that they would be there, nor why he has access to the same  that they do. A Mole would be suspected, and in fact all three previous films featured one in one way or another, but there isn't one. Given his Oddly Small Organization and that his official position in the Russian government was simply a scientific advisor, and how extreme his theories were, its hard to believe he's that well connected that he even knows who the IMF are, let alone how to play them like a fiddle and manipulate their every move.
 * Who shot up the car with Ethan and Brandt, and why? Sidorov eventually runs up and tells the shooters to stop. Were those guy cops?
 * Could've been Spetsnaz or something.
 * Presumably the police were simply aware that Ethan, an escaped man thought responsible for one of the most devastating terrorist attacks in Russian history, was in the car. Hence, they made the mistake of simply choosing to try to eliminate him instead of attempting a capture. As much as it paints the Russian police in a dim light, this scene makes more sense when you remember that they had no idea the Secretary was in the car and not just more dangerous American terrorists.
 * In Ghost Protocol, how was the cryptographer supposed to verify the launch codes at a glance? He obviously didn't know them already, and giving the codes a recognizable pattern kind of defeats the point of a password.
 * There aren't many people who can tease out those patterns in their head.
 * It's simple for codes to be practically impossible to guess but easy to verify. For example, if the launch code was a prime factorization of some number and you knew that number, then verifying the code would be nothing more than a multiplication, but as long as the number is large enough, you could never find the code just by knowing the number.
 * What was the point of Hendricks  for the Dubai deal? There didn't seem to be any reason why the real henchman couldn't have done it instead, and after all that's what henchmen are for. When his face was revealed to be an I.M.F.-style latex mask it seemed they were about to let loose a major plot twist, but it turns out it was just the Big Bad being eccentric.
 * While withing the context of the movie, it doesn't make much sense (not that eccentricities are unusual for Hendricks), but it seemed like a pretty clear attempt to show the audience, and Ethan, how devastatingly wrong the plan had gone without confusing all the different villains.
 * So who told the Russians in Dubai? Ethan?
 * Bogdan. That is, I don't think Bogdan told them, but they knew he and Ethan broke out of prison together, and were presumably keeping tabs on him in case he could lead them to Ethan.
 * Wouldn't NORAD's radar detect an SRBM incoming towards San Francisco?
 * I was secretly hoping for that too. Perhaps NORAD had just installed a new detection system and when they saw a single nuclear missile heading towards the US they assumed it was an error, since a preemptive nuclear strike would be all-out. They ignored it rather than do a retaliatory launch. It's happened before.
 * When the team realized the Russian cryptographer/scientist/nuclear codes guy was in Dubai, why not just let the meeting take place, than follow Winstrom and Moreau and capture them later, rather than take the risks of being recognized by following the original plan?
 * Is this movie just assuming there are absolutely no missile defense systems in the United States? And why even attack the United States with ONE nuke? If your goal is nuclear holocaust, wouldn't it make more sense to deploy multiple missiles to targets that don't have any defense systems or organized teams set out to foil you?
 * The goal with the first nuclear weapon was to get the U.S. and Russia to start fighting each other, Which presumably wouldn't take much. (The missile did in fact come from a Submarine, and with the kremlin bombing, Russia would be the obvious attacker.) (Of course, I have no experience with how nuclear policy works, so it may be the the one stray missile wouldn't have lead to anyhing, but the movie explanatiobn makes sense even with working missile defenses and one weapon.)
 * A magnet strong enough to carry the weight of a full grown man! Near COMPUTERS! How exactly does that work?