Goof: The aircraft carrier mentioned here is the USS Coral Sea. The last Coral Sea decommissioned in 1991 while this episode took place in 2003.
After finding out Harm will be judging the case, Harm and Mac discuss the time she was a judge. This refers to the episode "Ready Or Not".
Mac (to Bud): From now on, I'll let you be the one who objects.
Bill O'Reilly: Now, I don't know Commander Rabb. But he is a hero, a decorated fighter pilot, and he has not bailed out of this case.
Harm: Let's roll.
Mac: Excuse me?
Harm: Proceed, counselor.
Mac: Friendly fire. An innocent-sounding phrase. But there's another term -- fratricide.
Bud (reading a law book): A trial lawyer who becomes a judge is like a boxer who becomes a referee.
Sturgis: I've never had a judge hit me.
Harm: The day's still young.
Mac: It's a catch-22.
Harm: It's quite a catch, that catch-22. The best there is.
Mac: This is not a joke.
This idea for this episode was taken from the events of April 17, 2002, when an American fighter jet dropped a bomb on a group of Canadian soldiers conducting a training excercise near Kandahar, Afghanistan. In the real event, 4 soldiers were killed, and 8 others were wounded, some severely. The pilot was fined, reprimanded, and although he remains in the service, he is no longer allowed to fly.
When Harm says, "It's quite a catch-22 that catch-22. The best there is," he is quoting from Joseph Heller's book Catch-22.