Continuity mistake: After the Chitauri have arrived, Loki stands on the Stark Tower balcony and looks on New York. In this shot, Loki is standing facing the city directly, but by the next shot, he's suddenly standing 90° in the other direction with his head turned to the right, in order to be looking the same way as in the previous shot. (01:39:30)
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. (00:05:00)
Continuity mistake: There is a deleted scene of Steve Rogers looking through the files of his former comrades. When he first reads the sheet for Peggy Carter it has her address printed in a modern typeface on a label stuck to the page. The next time we see it, the details are the original typeface on the original paper.
Continuity mistake: In the fight scene between Thor and Iron Man, after Captain America tells Thor to put the hammer down, Thor slaps Iron Man, who is to Thor's right side, back several feet away from them and then jumps even further away. After Thor hits the Captain's shield, as they are all getting up, Iron Man is right next to Captain America and Thor, now to Thor's left side, (when he should be about fifty feet away and still to Thor's right side). Even if Iron Man made it back to Captain America before the shock wave, he should still have been visible before the shock wave for his position on the ground to be possible. (00:49:40)
Revealing mistake: In the scene where Iron Man and Thor fight, Thor begins to crunch Iron Man's metal arms so Iron Man fires at Thor and then headbutts him. In the shot from behind Iron Man, part of the green screen is reflected on the right side of his helmet. Can't be a tree or a bush because those are all dark green colored and the reflection is much lighter. (00:46:55)
Continuity mistake: 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. (00:25:20)
Continuity mistake: When Stark is about to fire up the arc reactor underneath Stark Tower, you can see that he turns for his approach. But when he is flying in with the nuke, Stark Tower is in a straight line with the street he flew in on - the same street as when they lit the arc reactor. (00:23:45)