Continuity mistake: Emily Sloane's left ring finger was shipped to Arvin Sloane in one episode in Season 2, when they are reunited in the Philippines, the left ring finger is bandaged and missing. Later, in the episode when she is shot, when she tells Arvin the CIA is listening, the left ring finger is there.
Continuity mistake: Season premiere, 'Authorized Personnel Only', part 1: When Sydney and the other agent are in the bathroom at the club, Sydney begins to smear black dirt on the agent's tee shirt for his punk transformation. The first smears that she applied differ when he exits the bathroom.
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Revealing mistake: In episode 3x10, Remnants, when Lazare shows up to talk to Will, we see that his left hand has been cut off. When Lazare is about to leave, he has his hands at his sides, and we can see that both arms are the same length, but the left one should be shorter, because it has no hand.
Character mistake: In season 4 episode 13, "Tuesday," when Marshall is meeting with Ulrich, he is both able to understand and reply in German. In season 5 episode 15, "No Hard Feelings," Marshall almost misses the opportunity to change the street light from red to green, because the text is all in German. Jack has to tell Marshall which word is green, indicating that Marshall does not understand the German language.