Continuity mistake: When Lemmy falls down from the window and running away from Bowser with Iggy, Iggy's face turns orange. Then later, it turns back to green.
Deliberate mistake: Season 2, episode 6 "Identity Crisis": When Bizarro starts decaying into the parody form of Superman, his costume goes with it; the blue fades, and even the 'S' insignia changes. Strange that superhero garments change right alongside their wearers when they suffer from an unstable genetic effect. Were the clothes cloned right onto his body, instead of sewn?
Continuity mistake: When Connie starts reading The Unfamiliar Familiar to Steven, she starts at the very beginning of the book. A couple cuts later, as she continues to read the same passage, the book is now open to the middle.
'Unmei no sentaku' mitaina - S1-E6
Plot hole: Akito's attack is point blank, on a ship part of a fleet with Distortion Field activated (basically, they have shields, like the good guys' robots). The explosion he causes is according to Ruri's damage report big enough that it managed to vaporize 80% of the ships they were facing, but his Aestivalis and the other 3 right floating nearby make out of it literally without a scratch. (00:05:10)
Coming Home - S1-E13
Plot hole: The logistics of the episode don't really make sense; Amuro's home village is held by (literally) a handful of Earth soldiers cut from their main force and that spend their time getting drunk and acting as occupation force, but Zeon has a full base (again, literally, almost) next door that sends reconnaissance troops and even aircraft to check for any activity at the refugee camp. There's no reason why the undisciplined and free soldiers would stay in such a dangerous position where they could be wiped out by overwhelming forces anytime, nor why Zeon would keep a pocket of the enemy forces that they can crush with ridiculous ease.
Battle Scars - S1-E7
Continuity mistake: When Echo prepares to calibrate the surgical pod, he has a bandage on his head, even though the members of the Bad Batch don't get their control chips removed until near the end of the episode. (00:14:11)
Continuity mistake: When Wakabayashi dives and catches the cross as it's still high in the air, Misaki and Tsubasa are to his right, then to his left. (00:05:15)
Other mistake: While Sonic and Tails are locked up in old Spelunk's cage during the cave-in, right before the huge diamondius crashes on top of the cage, there's a close-up of Sonic holding the bars, and the color of his torso becomes the same as the background mid-shot.
Bug Off/The Crawl Space - S9-E5
Continuity mistake: In Moving Away, Tommy tells the other Rugrats how they first met when Angelica lied about the nasty things they did. However in the Crawl Space, there is a flashback of Tommy, Chuckie, Phil and Lil playing in the playpen when they were younger. Chuckie is scared of the Jack-in-a-box in that flashback, so the Rugrats could not have met for the first time back then.
Coffee Quest/Phoenix Rises - S1-E18
Other mistake: In Phoenix Rises, when Phoenix runs away, the Big Coffee sign is missing.
The M.O.D.O.K. That Time Forgot! - S1-E2
Character mistake: M.O.D.O.K. refers to Hoobastank as "the Beatles of the late 90's." Hoobastank only released one album in the 90's, and they didn't become popular until after they released their second album in 2001.
Continuity mistake: When Lion-O lands after falling down the crevice after encountering the 3-Eyed monster the ThunderCat Logo on his is a red Lion on a black background, in all other shots it's a black lion on a red background. (00:07:30)
Plot hole: In each episode, Emmy, and Max travel to dragon land (often for a long time) without their parents ever knowing. This makes no sense. Their parents would notice sooner, or later that Max, and Emmy always go in, and out of the house, or that it's always quiet in Emmy, and Max's playroom. You'd think Emmy, and Max's parents would get suspicious, and would question their children accordingly.
Winning Through Intimidation - S1-E15
Continuity mistake: Panik's Metal Guardian can be seen on the field several minutes before he actually plays it. (00:10:30 - 00:13:00)
Continuity mistake: Chris says he is handing Heather the final marshmallow of the night. When the shot changes for Heather to yell at the rest of the team, Chris is holding a full plate of marshmallows.
Continuity mistake: I know that Animators re-use backgrounds but it is painfully obvious that when Keitaro and Narusegawa are leaving the exam results posting they walk in a straight line past the same "Ristorante" three times.
Twilight of the Apprentice - S2-E20
Continuity mistake: Near the end, when Ahsoka runs at Vader, for a split second when he turns around, the part of his mask yet to be sliced off is already missing.
Continuity mistake: In the episode where Fester invents a fabric: When Fester lies down on the parking lot, his head is first pointing upwards, towards a car, then in the next shot he has turned 90 degrees and his head is pointing towards Norman's legs.
Continuity mistake: At the end of the last series, Mario had brown hair, but in the opening shot of the intro, he has black hair. Also in this shot, the book on the table has the yellow rectangle on it five centimetres away from the top it, but in the next shot, it is three centimetres away. (00:00:03)
Deliberate mistake: When the news program is discussing Gyrich's assassination attempt on Xavier from the series finale of the original animated series, he's shown to have his classic look of auburn hair and sunglasses. However, when this scene occurred, Gyrich had black hair and was not wearing sunglasses. This was done deliberately to match the character design of the original series prior to the final 6 episodes, when Saban took over and redesigned much of the show's look.