Around 10:30 when Sheppard says, "First... It's a game...," a woman wearing a yellow top walks by twice, in the background.
Two different takes of Dr. Zelenka explaining to Sheppard and Ronon that the explosion left no residue are used with slightly different dialogue. It is a common movie custom - e.g., Rashomon (1950) - to have the same scene play out differently, to show that not everyone sees an event the same way.