• In this movie, the map of San Lorenzo is looking different than it did in "The Journal": the "UNKNOWN" area is much larger.
    • Strangely, in the "Exclusive First Look" video narrated by Craig Bartlett, the storyboard of the journal map shows it in its original state, though that shot has the changed map in the actual movie.
    • The map also appears in its original state once in the movie: when Arnold puts the glowing amulet next to it for the very first time.
  • Gerald's hair is missing a few blue lines in a few shots throughout the film.
  • When Arnold opens the journal during his dream, the entries are on the wrong order. The March 15 entry where Miles details how he met Stella is after the entries about their marriage and honeymoon.
  • At the start of the movie, the newspaper article of Lasombra on Arnold's wall has a different picture of him (the top of the hood is missing) than it does later on.
  • When the reanimated clip of "Field Trip" starts, Helga is wearing her new outfit instead of the old one, and the walls surrounding the lot are not red.
  • Before the home video starts, Eugene doesn't have the bandages and eye patch he has near the end of the video.
  • In the reanimated clip of "The Vacant Lot", Sheena is wearing her new outfit despite all the other characters wearing their old outfits from the original series.
  • In the reanimated clip of "Mugged", Brainy and the third teen thug are not there. Also, the teens did not actually back away from Arnold in the episode, they just ran off after he struck.
  • In the reanimated clip of "Harold's Kitty", Arnold and Harold are in front of the Sunset Arms boarding house, instead of Harold's house.
  • There are some character placement inconsistencies in the crowd after the video presentation ends.
  • When giving Arnold his passport, Grandpa says that the time Arnold's parents got involved with Lasombra was "practically the last time we heard from them". This is completely untrue; Miles and Stella disappeared when they went treat the sleeping sickness, as stated by Phil himself in both "Parents Day" and "The Journal".
  • When Grandpa is talking to Arnold on the runway and everyone else is boarding the plane, Eugene is not wearing his jungle outfit.
  • In the crowd during the parade in Puerto Clara, some characters from Hillwood appear (Mr. Hyunh, Mai, Torvald, the Jolly Olly Man, Monkeyman, and Robert) despite it not making sense. Gerald's head also appears in the crowd, but he's on the opposite side that he's supposed to be, and looks much taller than he should.
  • "Eduardo" says ¡Qué buen fortuna! when he meets Arnold at the dock. This Spanish phrase is gramatically incorrect, it should be ¡Qué buena fortuna!. "Eduardo" should not make a mistake when speaking Spanish, as he's a San Lorenzo citizen.
    • Helga also makes an error speaking Spanish when she meets the Girl Queen later on ("You don't suppose she hablas inglés?"), but in her case, it's justified, as Spanish is not her native language.
  • There are several design inconsistencies and other errors during the act aboard the Doña Marina. (Note: many of the errors are inconsistencies between the 3D model of the ship, which is being considered as the "correct" version, and the still backgrounds.)
    • In some shots, the interior part of the ship's hull (the area where the other ship's hooks grapple onto) seems to be made of wood planks, like the ship's deck, instead of metal, like the exterior part of the hull.
    • When "Eduardo" stands up after greeting Arnold at the dock, the staircase to go up to the captain's cabin is not there. Also, the cabin has a door and a handrail behind it, and the wall behind the steamstack has a door and a window (when they do not have those in other scenes), and the ladder to the crow's nest starts behind the captain's cabin instead of behind the steamstack.
    • During the buffet, Mr. Simmons has no animation, and Steve's skin is as dark as Paulo's. And when Harold gets off the table with a stomachache, an extra line appears on Rhonda's dress.
    • When Che lifts Olga, the ship's windows are much smaller than they should.
    • The shot in which "Eduardo" says "You must always be aware of the dangers here" is more saturated than previous and following shots.
    • After "Eduardo" says "I don't want to worry anyone", the tip of his nose is colored the same as his mustache.
    • The ladder to climb up to the crow's nest faces towards the ship's stern. But when Arnold looks up to see "Eduardo" using binoculars, when Helga sees Arnold climbing up at night, and in the first shot of Helga and Arnold up there, the ladder is facing the bow.
    • When Helga interrupts Arnold in the crow's nest, an extra line briefly appears in Arnold's face.
    • After Arnold finds the cabin empty while looking for "Eduardo", the next shot shows him going down a stairway. But he seems to be going from the steamstack level to the deck, when he should be going from the cabin to the steamstack level. (The next scene shows him on the steamstack level.)
    • At the very beginning of the scene where Brainy jumps into the river, the fog does not reach the left side of the screen.
    • After "Eduardo" leaves the cabin, an area on the left of the screen isn't lit up until Arnold looks out the window.
    • There's a looping error with the kids' animation in the sleeping quarters.
    • When Steve is fighting off the attackers, there's a ladder behind him which was not in any previous scene. Also, the second attacker he strikes is layered incorrectly; he should fall over the railing and down to the lower level, but he's layered behind the railing, making it look as if he falls through the floor.
    • When Che is fighting off attackers, the stairway to the captain's cabin is not behind him like it should; instead there's two metal ladders like the one in the shot with Steve. Also, the door on the left should not be there, and the one to the right does not go there.
    • "Eduardo" turns on the ship's white lights when he returns to the cabin. However, the red lights are not on when he does so, even though those are seen turned on in previous and later shots. Also, the white lights are not turned on in any later shots.
    • The map that falls in front of Arnold says "Selva Tropical of San Lorenzo" on the green square area. A more accurate descriptor would be "Reserva Tropical de San Lorenzo".
    • When the boat speeds up and the class falls down and spills onto the deck, there's an animation error on the door. Also, Curly, Stinky and Mr. Simmons aren't seen sliding even though they were seen falling down.
    • In the scene right after Rhonda says "Ugh! Who booked this!?", Arnold's shirt doesn't have its stripe, a handle on the ship wheel disappears and reappears as it moves, and in the scrolling background out the window, part of the sky is grey instead of colored.
    • During the sequence where the 3D boat is going through the rapids, Nadine and Mr. Simmons are on the starboard side, while Helga, Gerald, and Phoebe are on the port side. But there are a couple brief shots where their positions are switched. Also, Curly is never seen on the crow's nest of the 3D boat.
    • As the boat starts going down the rapids, the shape of the crow's nest briefly appears on the smoke column from the steamstack.
    • While Curly is up in the crow's nest, the hole that leads to the ladder is missing.
    • When "Eduardo" turns the ship wheel, part of his hair is not shadowed.
    • The metal pipe that Phoebe grabs onto during the rapids scene was not previously seen on the boat.
    • The underside of "Eduardo"'s hat is the wrong color for one frame after he kicks down the door.
  • When the steamboat explodes, Helga has no unibrow and Stinky's bag has no white spots. And after "Eduardo" reveals the river pirates were after Arnold, there's an error on Arnold's face. Also, when Helga looks angrily at Arnold, there's an error with her unibrow.
  • When "Eduardo" helps Arnold up, his mustache very briefly disappears as he turns.
  • When the class is entering the habitat, "Eduardo" is wearing a backpack instead of his machete bag.
  • The path leading to the habitat is much shorter when the class enters it than when Mr. Simmons and Arnold are in front of the gate.
  • Phoebe's ponytail disappears right before "Eduardo" reveals himself.
  • During the scene where "Eduardo" takes off his mustache and reveals he's Lasombra, the machete bag isn't on his back. However, he's suddenly wearing it again after the fade to black.
  • When Arnold kneels to apologize, Gerald's nose is colored white and part of his head isn't drawn.
  • After they escape, when Arnold shows Helga and Gerald the map, the white borders of the journal's pages aren't there, and the lower part of the map is cut off.
  • When the Flunky Guard begs Lasombra not to kill him, the guard with the white shirt is missing the grey area on his face (this also happens when the guard starts laughing alongside Lasombra shortly after), and the back of Lasombra's shirt does not have vertical stripes.
  • When Lasombra and the other pirates leave the compound to go look for Arnold, the Flunky Guard has the wrong clothes, and one of the pirates has a green shirt that should be white.
  • When Arnold puts the amulet next to the map for the first time, the map says "RAINFOREST BRESERVE".
  • The positions of the river pirates change between shots; as they walk towards the tile trap, the Flunky Guard is to the left of Lasombra, but after Lasombra steps on a tile, he's to the right.
  • After Lasombra drops the injured Flunky Guard, two cowboy hats hit by arrows can be seen on a tree in the background. However, the arrows actually hit one cowboy hat and one blue cap.
  • In the shot where Lasombra draws his machete to force the buff river pirate to go first, the rock face that was on the right before is not there.
  • When the pirates run after Lasombra into the tunnel, there's an error on the blue-shirted pirate's machete. Also, when the screen shakes due to the boulders falling, for a brief moment, the edge of the background can be seen on the left.
  • When Harold and Sid run out of the cage and get onto the platform, the Flunky Guard can be seen on the upper level of the compound's wall, even though he left with Lasombra earlier.
  • In several shots of breakout sequence, the ladder to climb up the water tower is not there.
  • In the scene after Big Bob tackles Che, Rhonda's hair looks already cut by a machete.
  • When Mr. Simmons says "Agenda! Coming through!", Rhonda can be seen (very briefly, to the right side of the screen) getting on the lift, but the previous scene showed her already driving the lift.
    • This error is actually caused by a reordering of scenes. In the original animatic, the scene of Harold on the lift came after the scene of Simmons running.
    • In that same scene, the green parrot with the red belly suddenly disappears right before the next scene starts. Also, the guard to the right of Mr. Simmons has a different shirt color; in this scene it's purple, but in previous scenes it was light red.
  • The guard who gets knocked out by Grandpa with the portable toilet door changes shirt and hat colors (the same colors as Lasombra) in two later shots: when forklift crashes into the water tower, and after the water tower falls to the ground.
  • In the scene where the top of the water tower rolls around and crashes into the power room, the forklift that knocked down the tower is no longer there. Also, the guard on the flying couch has his hat on, despite it falling off in the previous shot. Also in that same scene, Stinky and Eugene disappear while running away with Big Bob.
  • After Olga knocks down the piece of metal, there is a layering/coloring error on Eugene.
  • When Grandpa is calling for Arnold after the explosion, there is an animation error with Sid.
  • While looking at the murals of Arnold's parents, when Gerald asks about one, there's a brief error with the Girl Queen's head.
  • During the camera pan when Lasombra realizes there are only kids in the city, Helga briefly disappears when she's on the left edge of the screen.
  • In the scene where Arnold opens the Corazón, there is an error with the Corazón's faces: The "normal" face is in front initially, and when Lasombra draws his machete, the "angry" face is in front (likely because it detected Lasombra as an intruder). However when Arnold takes out his amulet and looks at the Corazón through it, the "normal" face is in front again, and when he presses the first button, the "angry" face is in front.
  • Lasombra's eyebrows change to a lighter shade of grey when he gets hit by the poison dart.
  • When Lasombra falls off the cliff for the first time, as he falls, he has scratches and his clothes are damaged, even though he was in perfect condition in the previous shot.
  • Lasombra's pupils aren't red when he says "Always so presumptuous." One of the stains on his shirt also disappears briefly. In the next shot, where Lasombra lunges at Eduardo, the inside of his mouth is green for one frame.
  • During the fight scene with the poisoned Lasombra, there are two instances (when Lasombra has a bag over his head, and when he grabs Arnold by the collar) where Lasombra's skin isn't sickly green like it should, and his clothes don't have stains, only scratches.
  • Right before Lasombra kicks the statue holding the Corazón, the relic is not golden. And in the very next shot, the face of the statue is happy when it was previously angry.
  • When the machine activates and creates a rain cloud, there's an error with how the shadow of the cloud expands.
  • When Arnold is running to see if his parents are waking up, there's an animation error with one of the Green-Eyes on the left side of the screen.
  • When Arnold reaches the entrance to the room where his parents are, the butterflies are incorrectly layered, making it look as if they're coming from the ground.
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