Corrected entry: Tony starts the movie with putting a number of sensors into his body, so that the Mark XLII knows where he and his limbs are. But neither Pepper or Killian have these sensors (it is ridiculously unlikely to assume otherwise) and yet the suit assembles perfectly fine on them as well.
Corrected entry: Air Force One explodes quite a while after the 13 people have been sucked out near the tail section of the plane. During the delayed (15+ seconds) explosion, you can see lots of debris falling with smoke trails. The problem: During the rescue, as Iron Man is catching the free-falling victims, you can see many debris trails that have already fallen below past the victims. This defies Newton's law of gravity regarding items, no matter their weight or size, will all fall at the same speed, (even when you factor wind resistance). Even with arms and legs extended, all of those people would not have slowed down enough to allow all that debris to pass, especially with the head start they had.
Corrected entry: When Ellen Brandt handcuffs Tony in the bar, his hands are behind him. After being chased into a kitchen area and fighting, his hands are now handcuffed in front of him.
Corrected entry: Pepper is in hospital with an IV line in her arm. A nurse comes in and injects a drug into the line. The problem is: The nurse doesn't kink the line above where she injects, which means the drug can go up the line and into the IV bag as well as going down the line. When a drug is ordered IV, the doctor who ordered the drug wants it to go in quickly, not slowly from the bag or upper tubing.
Corrected entry: Jarvis tells Tony that crews have arrived with cranes to start removing debris to reach the basement lab. With the number of suits stored there why couldn't the suits just dig or blast their way out under remote control? 99% of the house fell into the ocean so there wasn't so much rubble that the suits couldn't free themselves.
Corrected entry: The explosion of a failed Extremis subject is so strong it vaporizes living organisms in the blast radius along with collateral damage (as shown at the Chinese Theater). In Tennessee, the site of a similar incident, it is shown that the crater of the explosion is a few feet from the corner of two walls. The walls, for some reason, were not obliterated even though the explosion was strong enough to destroy everything else.
Corrected entry: When Tony first meets Trevor, he holds him at gunpoint with a semi-auto pistol. After thinking that he's a decoy, Tony racks the slide of his pistol and asks where the real Mandarin is. No bullet comes out of the pistol when Tony racks the slide, meaning that it wasn't loaded when he was initially threatening Trevor. Considering that Tony is an experienced weapons designer, there's no way he would've been roaming through the heavily armed enemy HQ holding an unloaded gun. (01:15:50)
Corrected entry: The "Igor" armor was last seen supporting the damaged platform and preventing it from collapsing. After Tony orders the Clean Slate Protocol which destroys all the armors, this should have included Igor, which would mean the platform should have collapsed and put Tony and Pepper's life at risk.
Corrected entry: During her fight with Killian, Pepper tore off the arm of a random Iron Man armor and fired a repulsor blast at a mini missile, thereby killing him. How was Pepper able to control the arm? Without a helmet, she didn't have any neural interface with the armor and unlike Tony, she didn't have any implants that would have allowed her to communicate with the armor. In addition, where did the arm get the power to fire the repulsor blast? There was no connection between the arm and the ARC reactor in the chest of the armor.