Audio problem: When Luke says, "Now all we gotta do is find this Yoda, if he even exists," if you look closely, his mouth never moves.
Audio problem: Before the trio crashed into the Daily Planet (just before the battle with Supes), they were heard flying outside the building. For 3 superbeings with the ability to fly unaided, they sure sound heckuva lot like jet-propelled aircrafts. Jet aircrafts are noisy because of their engines, but superpeople?
Audio problem: When Benson is dismantling Hector and putting his brain in the container, he says 'What you can't stand, you run from,' but his lips don't match what he says. (00:48:50)
Audio problem: When the Kelvin sacrifice themselves in front of the Sonic Tank, Cowboy walks off and says, "C'mon, lets go", but his lips don't match what he says.