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The flashback Batgirl and Batman both have their revamped designs from The New Adventures of Batman. However, the Joker has his classic design from the Batman and Robin Animated series.
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Having a second Batsuit would make more sense. After all, in the pilot episode "Rebirth", the one Bruce wore was certainly a larger size. It would look very loose on Terry's slender frame unless it had the ability to adjust itself. There's the possibility Bruce redesigned the suit to better fit Terry after the episode "Lost Soul" if there wasn't a spare costume at the time.
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The design on the chest of Nightwing's costume is red in one scene, when it should be blue.
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In "a Touch of Curare" Gordon mentions that Dick Grayson left. Here, Gordon says Batman forced them to hang up the tights, but does that include Nightwing?
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Tim Drake is the second Robin for this version. The character Jason Todd is not mentioned in the universe Warner Bros. Animation has created.
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The voice of Angie Harmon, who plays Barbara Gordon, is not suited for character of such an age. Stockard Channing, who played Gordon in the series, sounds very different from Harmon creating a discontinuity in the movie.
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In the opening credits, both of the Executive Producer credits are misspelled "Exectutive".
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Zeta doesn't look like he did in the episode "Zeta," although Batman doesn't even notice that.
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When the Kobra crew leaves the loading bay, they use a laser to cut the door leading into the building. However, when they return there, isn't a mark on the loading boy door.
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In this episode, Charlie "Big Time" Bigelow works for The Major, voiced by Jon Polito. In the movie The Rocketeer, Jon Polito played Bigelow, owner of Bigelow's Air Circus.
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How does Batman plan on getting back to Gotham City at the end? He turns around and walks off into the Arctic, which is kind of dramatic. However, the Batmobile has been destroyed and he has no way back! (Reply: Well, he is walking towards the crashed Batmobile. Maybe he hopes to be able to use it again.)
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Even if the possessed Superman had to wait to initiate his plan (whatever the heck it was that required calling in Batman and destroying Metropolis) until it had bred enough other starfish, why didn't it use some of the first few to take over the remaining JLU members far earlier?
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So why did the possessed Superman launch the attack on Metropolis in Part 1?
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How did Warhawk escape from his armor? The events of Part 1 seem to make that it very difficult, if not impossible, for him to have done so. And why didn't Terry see Warhawk exit his armor on the replay?
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When Superman spins Inque around everywhere, there is a goof. It shows Terry step and hold Inque on the ground. When he sees that the innocent bystander is really Superman, it shows them both in a full screen shot, but Inque has somehow vanished from the scene.
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The name of the splicing agent, 'methyl glycose', is erroneous, in that in the story it is an enzyme, but its name denotes that it is a sugar. Enxymes have names that end in the '-ase' suffix, whereas sugars end in the '-ose' suffix.
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When the Repo Man scans each of Deanna's credit cards, he swipes the plastic part of the card through the scanner and not the black magnetic strip.
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In the scene where Inque escapes from the office, she is shown moving right through a solid glass window without it breaking.
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All except the beginning, Shriek is not wearing the device that gives him hearing, but he can hear everyone.
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Trivia: When Payback attacks Warren's store, look at the till - apparently, they still use paper money as well as creds.