Continuity mistake: Charlie, Olivia's former partner and friend in the FBI shows up in this episode during the interview with Mrs. Rusk, but Charlie was killed off by one of the shapeshifters in a previous episode, and the shapeshifter that killed Charlie was himself killed off by Olivia, who in other episodes reflected back on killing him. This episode was supposedly meant to be in season 1 as ep 21 or 22. Unknown why they didn't air it then, and decided to put it in the middle of season 2 (for no apparent reason).
Other mistake: The battle droids - including the commando droids featured here - habitually have two broad fingers and a thumb. So how can a commando droid squeeze itself completely into clone trooper armor without its broad fingers tearing open the gloves, since it can't separate its fingers?
Continuity mistake: All shots of the Jeep Cherokee prior to it crashing (and during the process of flipping over) show that it wears factory-optional silver steel wheels of a 'star' style. But as the wreck settles upside-down, it's wearing plain steel wheels (like those found under full wheel covers or on a spare tire).
Revealing mistake: During "Brand New Day", watch the background as Dr. Horrible appears as a giant and stomps down the city-street. As he takes his first step, a piece of concrete from building to his right falls off and hits the ground. However, if you look closely, it's obviously a quickly-made computer effect. As the piece of concrete hits the ground, it simply vanishes, and is replaced by a rather odd-looking animated "poof" of dust. The issue is the concrete piece was much bigger than the cloud of dust, so it's clear that the piece simply disappears right as the dust-poof appears.
Triumvirate of Terror! - S3-E8
Continuity mistake: When Joker zaps Wonder Woman and her mother, they are both standing in front of their thrones and fall forwards. But when Wonder Woman stands back up, her mother, still unconscious, is suddenly off to the side and behind the thrones. (00:11:35)
Audio problem: They went to an investigator to let him listen to the audio. The audio with the woman screaming and the gasp, the gasp was Zak, not another apparition.
Continuity mistake: When Domino is playing pool, in the wide shot, she is shown at the one of the corner pocket sides of the table, with Toad perched on the left corner pocket across from her. When the shot changes to her getting ready to take her shot, she is now standing on one of the side pocket sides of the table, with Toad similarly perched on the corner pocket on the left across from her, only now it would be on the same end of the table where she was originally standing. (00:21:57)
Containment - S1-E5
Continuity mistake: At the end of the episode, when the bad guy is preparing the syringe of small pox, he follows the usual method of tapping out any air in the tube - when he is shown injecting himself, a large air bubble is back in the syringe (which would probably kill him quicker than the smallpox).
Continuity mistake: The Army Humvee arrives in Piedmont and finds the townsfolk all dead. The timecode on the truck's video recording is 22:13 hours. When the team gathers to learn of the situation, they are shown this video. The General then presents a video he says is 2 hrs later, the view from the drone with infrared film. The time code on this, is 3:15. Both were shot in the same place, and both would be local time, so the time is wrong. More to the point, the original drone footage did not have any timecode on it. (00:18:40)