Continuity mistake: When Maria Hill is being attended to after she gets hurt, her earpiece is on the left side of her face. In the next shot she is talking to Nick Fury and her earpiece is on the right.
Continuity mistake: This is just after Coulson walks into Stark's office and hands Pepper the file on the Avengers, which she promptly passes on to Stark. In the front shot, she is holding the champagne glass down by her waist. Cut to the shot from the back and you can see the glass just above her right shoulder.
Factual error: During the scene on the Helicarrier where Bruce Banner "Hulks out" and jumps at the F-35B hovering just outside, we see the F-35B fire its guns, one inside each of its intakes. The F-35B has only one gun, externally mounted to underside of the fuselage. It would be impossible to mount a gun inside an aircraft's intakes.
Continuity mistake: When Tony arrives at Stark Tower, he and Pepper share a bottle of champagne. In the shot where he says "Next building is going to say Potts on the tower", Tony's champagne glass is in his hand and there's no sign of another glass several inches either side. In the next shot, Pepper's glass is suddenly 2 inches away.
Continuity mistake: During the big battle against the Chitauri, Captain America is zapped with a blaster bolt. When Thor helps him to his feet we can see a significant amount of damage done to his suit, just below the star on the right hand side. But later on after Iron Man destroys the Chitauri ship with the nuke, the damage is completely gone.
Continuity mistake: After the big battle, Iron Man lies on the street when Capt. America, all dirty and messy, says "We won." Iron Man sighs in relief and rests his head on the pavement. A frame later, from a wide angle, his head is raised, plus Capt. America's face is clean and his hair is brushed.
Continuity mistake: In the scene where Loki escapes with Hawkeye and Agent Hill is chasing them, she does a 180° spin and ends up face to face with Loki's driver. She shoots through the glass and you can see the bullet hole, but during the rest of the scene, the hole is gone, or moved to the passenger side.
Revealing mistake: In the scene after the Chitauri army enters the atmosphere, they start shooting people in the ground and in the next shot if you see underneath the bridge there is a restaurant with people running around to avoid getting hurt. If you see there are two glasses of wine and some food plates sitting in a table firmly which does not even move despite the blast wave that was created from all the shooting in the ground near it.
Continuity mistake: After the Tesseract opens up the portal that Loki enters from, 4 SHIELD guards are seen slowly advancing on his position. On the left side of the device, two of them are moving. The one further behind walks over an area of the floor that is illuminated by some orange light. The shot cuts to his feet, and suddenly the floor is dark.