Other mistake: Slightly after the opening credits, Jack Malone is investigating the disappearance of Annie Miller and is standing in her mother's bedroom. He turns to Carol Miller's boyfriend and asks to "speak to Mrs. Malone alone." The subtitles correctly have 'Miller' written, but when Anthony LaPaglia says his line, the two words rhyme.
Continuity mistake: In the episode "Lost Time," when the professor stands up in the holding cell after Jack tells him that someone saw Skye at 10:30, he slams his chair back causing it to tip over. In the next shot the chair is upright, then when he goes to sit back down, it is again on its side.