Continuity mistake: When Gillian and Eli talk with commander Markov about what happened with the X-48, he says "I was at the cruising altitude of 10,000 feet... Actually, ten-thousand-five."When they play back the recording, Markov says "actually, ten-thousand-five-hundred."
Continuity mistake: Season 2, Episode 21: "Darkness and Light" - When Cal goes to tell Mr. Dawkins that his daughter has HIV, he brings a glass of water into the room with him. The glass is half full (or half empty, depending on how you look at it), but throughout the scene it keeps switching between half full/half empty and three quarters full/one quarter full.
Continuity mistake: Season 2, Episode 20, "Exposed": In the warehouse where Dave is being tortured, Cal says to Moon that he should get Dave to talk about shagging his mum. Moon then points his gun at Cal. In the shots of Cal the gun is held "gangsta style", i.e. horizontally. But in the shots of Moon the gun is held vertically.
Continuity mistake: Season 2, Episode 20, "Exposed": In the scene where Emily finds her Grandma's diary, she leaves a message on Cal's phone about them having lunch together. As she hangs up, her fringe is tied back behind her right ear and falls down in front of her face, but in the next shot it is back behind her ear.