Continuity mistake: When Tony and Pepper are attacked by 3 missile-wielding helicopters, Tony, dressed in his metallic suit, has blood on his nose and cheeks. Problem is: The blood increases on his face, which is normal as it is still bleeding, but then it lessens. Then it gets worse again. (00:37:45 - 00:38:45)
Revealing mistake: When Tony and Rhodes are on the oil tanker bunkered behind an obstacle, Tony realises his gun is empty and asks Rhodes for a new magazine. When Tony ejects the magazine you can see that it is actually an airsoft gun magazine; thus exposing that it is actually a prop gun.
Continuity mistake: When the Mark 42 is "done" assembling for the first time, in Tony's workshop, a digital model of the suit appears in the lower right corner of the screen. In this render, the suit is complete, but a moment later there is still one piece missing, which hits Tony so hard the entire suit falls apart. (00:07:30)
Character mistake: Killian tell Pepper the "primary somatosensory cortex" is the pain center. However, this is a gross exaggeration someone of his knowledge would not say. One, the area handles all tactile (touch) receptions. And two, other areas of the brain handle pain, so there's not a "pain center." However, the area that lights up is also wrong, because only the right side would be stimulated since it was his left arm that was touched.
Continuity mistake: When Tony leaves the bar, his hands are cuffed behind his back. When he is shot at in the next scene after jumping through the window, his hands are somehow cuffed in the front of his body. (01:54:50)
Continuity mistake: When Tony is attacked by helicopters in his Malibu mansion, his right hand has a black wrap around it. After he gets buried by rubble underwater in the suit, his right armored hand detaches and grabs his bare right hand to pull Tony out from the rubble. Tony's bare hand no longer has a black wrap.
Character mistake: When Happy is in hospital, two bad things happen: One, when a nurse comes into the room, she injects a drug into his IV line, but she doesn't kink the line above where she is injecting, so the drug goes both down and up the line. Two, Happy's IV line isn't attached to a pump. The nurse manually fiddles with the flow rate of Happy's IV. But the fiddling leads to nowhere, as she doesn't look at the chamber where the drops come out - this is very important, as the IV bag can run out anywhere from 30 mins to 3 hours.
Continuity mistake: When Tony and Rhodey first get noticed as they search the oil platform, one of the Extremis soldiers starts shooting at them. They dodge the bullets and hide. Tony then says "You see that? Nailed it" and he is shown to be looking at Rhodey. Next shot, he's suddenly looking downwards. (01:41:15)
Other mistake: Immediately before the helicopter attack on Tony's house, Maya (the "botanist") looks at the TV set, which shows a news chopper shot of the home, and says "Should we be worried about this?" It's only a moment later, when everyone looks at the screen, that a missile track appears on the screen.