Continuity mistake: In the first Avengers briefing with the Secretary, the shot has Tony Stark sitting in the back with a wedding ring on. The shot changes to another view and Tony is sitting in the same location, but is no longer wearing a wedding ring. This continues many times within the scene.
Factual error: Shortly before the EMP bomb is activated, the crate containing it is shown. "Diese Seite Oben" is painted on the box, which is a bad translation of "This side up." In Germany crates only use the word "oben" to indicate the upper side of a box.
Continuity mistake: While Cap is fighting Crossbones, the items on the table behind them change between shots.
Continuity mistake: In the opening sequence, the courtyard outside the lab is filled with bodies. Scarlet Witch pulls the gas out of the building and sends it into the sky. We then get a wide shot of the gas and in it the courtyard is completely empty of bodies, including Wanda and Falcon. (00:07:18)
Continuity mistake: While the sink is filling in the interrogation scene, the water is running over his shoulder, however when the camera shifts above, the faucet is not close enough to have water running over him. (00:25:00 - 00:27:00)
Continuity mistake: The end of the movie shows the jailed Avengers with their wounds still visible, while the others at the Avengers compound are mostly healed, including Rhodes.