This episode is dedicated to Jeff Upton, who up until his death worked as 'Chief Lighting Technician' on the series.
In the original story idea, it was to be Teal'c charged with a crime he didn't commit. As Teal'c already had a significant story arc for the season, it was changed to Mitchell, in order to explore Mitchell's past.
The main computer terminal which is used in the alien lab is the same terminal that Samantha Carter uses in Revisions (2003).
Most episodes of Stargate SG-1 (1997) begin with the discovery of a conflict, but Collateral Damage (2006) begins with a preview of an incident from within the episode then, after the opening credits, goes back to the beginning of the storyline.