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).
Continuity mistake: During "Brand New Day", at one point, Dr. Horrible stabs a picture of Captain Hammer attached to a dartboard with a handful of darts, all right in the center of the picture. A few shots later as Dr. Horrible sits, suddenly the darts are far-more spread out. (It's in the background and can be hard to see, but it's noticeable.)
Triumvirate of Terror! - S3-E8
Continuity mistake: After revealing himself to Wonder Woman, Joker rips of his cross-dress disguise. The two halves land on the ground on both sides of him. But then when he subdues Wonder Woman with his Joker gas, he is standing in the same spot, approximately, and the torn clothing is now gone. (00:12:00)
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.
Audio problem: When Toad is saying "Who are you calling a perp? This is messed up. You don't know who you're dealing with," his mouth movement is slightly out of sync with the dialogue. (00:01:00)
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)