Continuity mistake: Throughout the film, Tony Stark's chest ring can be seen glowing through his shirt except for two occasions when it's suddenly off - after Loki escapes from the helicarrier, and when Loki and Tony Stark are talking in Stark tower, even when he's wearing the same shirt.
Continuity mistake: When Hawkeye is breaking onto the Helicarrier, he and some snipers break down a duct cover and enter. When the cover lands on the floor, it is resting away from some pipes with some slats missing. As soon as Hawkeye enters the duct, the cover is now resting against the pipes, and the slats have reappeared.
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: When Tony goes after the nuke, there is a huge cut visible above his right eyebrow (or viewer's left). Later on after his face mask is removed, his right eyebrow is completely visible in the shot, even with the helmet in the way, and the cut is nowhere in sight.
Continuity mistake: When Captain America, Black Widow and Hawkeye are fighting their way through the Chitauri in the S.H.I.E.L.D. jet, one shot shows the Chitauri blasting at the jet causing part of the front of one side to get blasted and a burn mark is left on the jet. A few seconds later, Loki blasts one of the engines and the burn mark on the front of the jet has vanished.