In "Strong Badathlon", Strong Bad's arm disappears briefly when he wipes the sweat off his forehead.
In "Nightlife", during the scene where Strong Bad is talking to Bubs at the bar, various parts of the bar change different shades of white during different shots.
In "Email Thunder", when Homestar puts cinnamon on his face, his eyes are the wrong size. They're quite noticeably squished and placed too high on his face.
In "Hygiene", when "John" looks in the mirror, his reflection blinks a split second after his counterpart.