When Megatron shoots Optimus Prime he shouts "Fall! Fall!". However, the lip syncing on Megatron is out of place as he says it, instead hinting by the animation that he would've originally said at least three words instead of two.
During the voting process to keep the wounded on board Astrotrain or dump them into space, the voices of the Decepticons chanting "Aye!" and "Nay!" don't match any of the Decepticon characters present.
When Hot Rod suggests that Kup has better things to do than tell stories to the Dinobots, the Dinobots begin protesting. One of them says, "Quiet! We wanna hear story!" It looks like Sludge's mouth is moving here, but this definitely isn't Sludge's voice.
When Optimus Prime transforms into his truck mode, he takes an inordinately long time to complete the transformation. He is still completing his transformation long after the transforming sound effect is heard.
After Rumble and Frenzy shake Devastator apart, Devastator's components transform back into the Constructicons. We don't hear any transforming sound effects when this happens, though, even though we see Devastator's shoulders fall and transform back into Hook.
The size of Unicron in general changes in various parts throughout the film. The first planet attack shows that Unicrons mouth is large enough to almost swallow a planet whole, however during his first conversation with Megatron when we can see the two characters from a side on angle, Megatron appears to be nowhere near as tiny as he should be in comparison to Unicrons mouth.
In the scene where Hot Rod successfully opens the Matrix, he is able to fit his fingers into square holes in the handles. These finger holes do appear in a couple of other scenes (when Galvatron claims the Matrix from Magnus, and when Galvatron tries to claw it open to use against Unicron), but they seem to be an afterthought. The finger holes are missing throughout most of the movie, including the scene in which Optimus Prime first takes the Matrix out of his chest.
We watch Prowl die with flames beginning to shoot out of his mouth, and eventually he falls on his back with his whole torso in flames. Later, as the Decepticons take over the controls of the Autobot ship, the remains of the four autobots are seen on the floor, and Prowl is lying face first with much of his torso still intact. In fact, very little damage is shown on all four fallen Autobots until Ironhide reaches for Megatron in desperation.
Sunstreaker is seen doing road construction early on in the movie, he is present amongst the Autobots setting up the roadblock for Kup. He is also seen next to Kup when he sees Hot Rod shooting at the shuttle. Yet later in the movie, he is seen piloting the shuttle that Optimus Prime has taken to arrive to Earth, and is standing next to him as he transforms to go face Megatron.
In the scene where Hot Rod and Kup are fighting the Sharkticons, right before Hot Rod punches the Sharkticon in the mouth, the entire top sections of Hot Rod's shoulders are colored grey. Only the panels inside his shoulders should be grey.
There are several continuity errors during the above scene. As the ship lands, we see a very brief glimpse of the ship's cockpit from the outside, after which we cut to a scene from the inside of the cockpit, looking outside the windows of the ship. In the scene from inside the ship, Grimlock is standing in a different place; the window divider has moved; and Wheelie is sitting instead of standing. Also, Snarl can be spotted (also in robot mode) in the exterior shot of the cockpit, even though he wasn't there with the Autobots who boarded the ship, and disappears again after this shot.
When Optimus Prime drives right into the ranks of the fleeing Deseipticons in truck-mode, you can see the reflection of Thrust's terrified face in his truck-grill. The problem here is that Thrust is a really tall robot, and there is no way he could see himself in Prime's relatively low truck-grill. In this scene, all of the Deceipticons seem to be quite small as Optimus plows through them.
When Sounwave deploys Rumble, Frenzy, Ravage and Ratbat to jam the transmissions being made by Blaster, we can see for a few seconds from a side angle that Rumble and Frenzy are the same colors, red and black. This is an animation error as Rumble is normally a light purple, which he returns to in the next shot.
When Unicron transforms, the Autobot Matrix of Leadership disappears from Galvatron's neck, who has been wearing it like a necklace, and is seen with it again when the sequence is over. Unicron's head design also changes drastically in subsequent shots. This whole scene was in fact one of the first to be animated, when Unicron's features and the story outline altogether have not been finalized yet (also explaining the absence of the Matrix from this scene).
In a high angle shot of the battle above Autobot City, Shockwave can be spotted among the participants of the aerial melee, when he is supposed to be on Cybertron. Dirge is also colored like Ramjet in this scene. Not only that, but Rumble can be spotted flying away to the left, but he is colored like Shockwave. Also in this same scene, Reflector appears, but he is colored like Ironhide. This is particularly interesting, since Reflector was phased out of the cartoon early in the second season. In fact, Reflector appears three more times in the movie, all erroneous appearances.
In one scene, Optimus Prime calls up Jazz on his monitor to have him check for Decepticon activity. After Ironhide's shuttle launches, however, there's a scene with Jazz and Cliffjumper standing right next to Prime.
In the final camera pan of the victorious Autobots on Cybertron, both Blurr and Perceptor are missing their Autobot symbols, and Jazz's front bumper and top chest panel are both colored white again. Then, in the next shot of Rodimus Prime thrusting his fist into the air and proclaiming, "Till all are one!" the nose on his Autobot symbol disappears.
After the Autobots successfully escape into space, during the first scene inside the shuttle in which Kup is telling stories to the Dinobots, Slag is missing the Autobot symbol on his Triceratops head.
When Jazz first appears on Optimus Prime's monitor, he is missing the Autobot symbol that's usually on the square blue panel on his chest. The symbol is missing again, when he contacts Moon Base Two, and again when Cliffjumper begins the countdown for the shuttle launch.
As Cliffjumper begins delivering the countdown for the shuttle launch, the top of his body is colored light blue, as though this were his rear windshield, when his body should be red. Also, Jazz is standing next to him and the front bumper on his chest is colored white instead of red.
As Optimus Prime, Jazz, and Cliffjumper are watching the shuttle depart and Prime comments, "Now, all we need is a little energon and a lot of luck," the inside of Cliffjumper's helmet is colored grey, like his face, instead of red.
Also, right before Soundwave transforms to tape deck mode to play back Laserbeak's recording, there's a computer monitor to the right of Soundwave which is rectangular with an indentation on the left side. After Soundwave transforms and plugs into it, however, the viewscreen is perfectly rectangular with no indentation.
After Megatron finishing watching the recording and comments than Prime will need more luck than he imagines, the bottom triangles of Megatron's Decepticon insignia are connected to the rest of the symbol. They are supposed to be separate pieces.
As Megatron rips through the breach in the shuttle, we see Scavenger behind him, whose body and head are colored entirely purple. Scavenger should have a green body and a black helmet with a grey face mask and red eyes.
Finally, when Shrapnel collides with Blitzwing, the underside of Blitzwing's tank mode is tan and featureless. Compare this to earlier, when he transformed into his tank mode and his purple robot-mode chest was still visible on the bottom of the tank after he finished transforming.
As Blaster begins sending his distress signal to Optimus Prime, in the group shot of the Decepticons firing on the city, Soundwave's head is miscolored. The panels on the sides of his head are colored blue, like the rest of his helmet, when they should be grey.
As the Decepticons charge the city and the truck-mode Prime approaches them from behind, Soundwave's upper legs change from grey to blue, and Blitzwing's head changes from yellow to purple for a moment (as mentioned above). Dirge is also colored like Ramjet in this scene.
After Megatron throws that shard of metal into Optimus Prime's side, as Prime is clutching his wound, we see the little triangle on Prime's forearm on the outside of his wrist (facing front). In the next scene, when Prime back away, the triangle is now on the top of his wrist (facing up).
When Magnus responds to this decision by saying, "I'm not worthy," the components on either side of his head are colored grey, like the antenna attached to them. They should be blue, like the rest of his helmet.
As Starscream is dusting off his hands, part of his chest armor is colored grey when it should be red. Then, when Starscream is nominating himself to be the new Decepticon leader, the entire middle section of his chest is colored orange again.
When the cassettes eject themselves to defend Soundwave's play for leadership, Soundwave is missing the red stripes around his wrists, and the border around his cassette door is light blue when it should be yellow. Also, the door remains open for this shot, when it normally closes back after the cassettes have been deployed.
After Galvatron shows up on Cybertron and takes command, Soundwave is drawn significantly off-model as he cheers the arrival of the new leader. The cassette door in his chest is incredibly small in this scene; it is not much bigger than his head.
As Spike and Bumblebee celebrate Unicron's apparent destruction, the symbol on Bumblebee's chest is missing. Then, when they realize that Unicron is still intact, Bumblebee's open mouth is colored red, when it should be grey.
After the shuttle begins to taxi and Arcee starts running after it, at one point she actually reaches the ramp, and it even looks like she grabs onto it. In the next scene, though, she is several feet behind the ramp again.
After Ultra Magnus orders the separation of the ship, as Perceptor swivels around and proclaims, "That's too dangerous!" the entire front panel on his forehead is yellow. Only the rectangular box inside this panel should be yellow.
When Hot Rod is trying to save Kup from the giant robot squid, Hot Rod retracts his fist and replaces it with a buzzsaw blade. After he uses the blade on the squid for the second time, his hand suddenly reappears. A moment later, the buzzsaw blade is back again; then Hot Rod finally retracts the buzzsaw blade and replaces it with his hand.
A moment later, in the shot of the Autobots scattered around the cabin of the shuttle, Blurr's entire head is grey. It should be colored light blue with a light grey component on the back of his helmet.
As the Dinobots proceed through Quintessa, Slag nearly walks into a trap door, and Grimlock whacks Slag out of the way with his tail. In this scene, Slag's lower jaw is round in shape. When Slag gets to his feet, he growls at Grimlock and bares his teeth. In the scene after this, though, Slag's jaw is back to its normal square shape, and he once again has no teeth.
As Wheelie first approaches the Dinobots, Slag has a yellow square on his forehead instead of his Autobot symbol. Later, when Wheelie climbs onto Sludge's back, Slag has a yellow circle on his head instead of the Autobot symbol.
At one point during the battle on the Planet of Junk, Wreck-Gar throws his axe at the helicopter-mode Springer, and it goes tumbling off into the distance. A moment later, though, Wreck-Gar engages Springer in robot mode, and his axe has miraculously returned.
When Hot Rod emerges from the Quintesson ship, the ship is colored silver in the matte painting behind him, but in the animated shots before and after this scene, the ship is its normal green color. Also, the symbol on Grimlock's dinosaur mode chest is missing as he exits the ship.
In the long shot of Unicron standing on Cybertron, battling the Decepticon fleet, he suddenly seems a lot smaller than he did when he first approached Cybertron and raked its surface with his hand. Also in this scene, Unicron is shooting pink-colored beams from his functional eye. In the close-up, however, the beams he is firing are green in color.
During the Dinobot attack on Unicron, when the camera pans up to Unicron's head, his damaged eye is inexplicably intact. Also in this scene, when Swoop is attacking Unicron, he's missing the Autobot symbols on his wings.
When Unicron reaches for the Dinobots and tries to close his first on them, the square panels on his knuckles are light grey when they should be colored orange. There is also a pretty huge size discrepancy in this scene. When the Dinobots first start attacking Unicron, they are much larger than they are a few seconds later when Unicron tries to grab them.
When Hot Rod crashes the Quintesson ship through Unicron's eye, it makes a hole that extends from the top of his eye to the bottom. When we cut to the inside of Unicron's head and see the ship traveling into his head, though, the hole has changed size and is now considerably smaller.
When Daniel is trying to activate the laser on his exo-suit to save Spike, the panel on the arm of his exo-suit is already open. In the next scene, the panel is closed; then Daniel fiddles with some controls and the panel pops open.
When Daniel fires his lasers from his exo-suit to the lid of the Vat inside Unicron we get a brief glimpse of the Autobots falling, showing Spike, Bumblebee, Jazz and Cliffjumper followed by a second Bumblebee.
After Daniel goes down the waterfall inside of Unicron, he is shown washed up next to the acid vat. However, after showing a few robots being dropped into the acid, Daniel is shown running up to the vat from the water.
The two Autobot shuttles have different color schemes. They are both predominantly orange, but Ultra Magnus' shuttle has red trim, while Hot Rod and Kup's shuttle has grey. When Magnus' shuttle takes off, though, it's got grey trim instead of red.
There are a couple frames where you can see the inside of one of the Lithonian ships being devoured by Unicron. The pilot of the ship appears to be Kranix, even though he apparently screams out Kranix's name, and Kranix appears later in the Quintesson prison.
The voice actor credits include listings for the characters Inferno, Gears, Prowl, and Dirge, even though none of them had speaking lines in the movie. Also, Jack Angel does not receive a credit for the character of Ramjet, even though Ramjet's voice can clearly be heard during the scene when the injured Decepticons are pushed off of Astrotrain and he commands, "Get! Make room for others!" For that matter, Frank Welker doesn't get a credit for his portrayal of the auto-combatant that Hot Rod is sparring with. The cast list is supposed to be alphabetical, but Peter Cullen's name is listed before that of Scatman Crothers.
Astrotrain can apparently change his size to be able to accommodate all the other Decepticons (who are generally about as big as he is) inside himself when he transforms into his alternate modes. This strange phenomenon is called "mass shifting", but one particular scene takes it to the extreme: The Constructicons merge to form the gigantic Devastator, inside Astrotrain. This is considered to be an error, since for the Constructicons to be able to unite, Astrotrain would have to grow immensely huge, bigger than even the inconsistent senses of the Transformers cartoon would allow.
When Galvatron interrupts Starscream's coronation Thundercracker and Skywarp and some Insecticons can be seen clearly among the Decepticons there. Thundercracker, Skywarp and the Insecticons were among the damaged Decepticons thrown from Astrotrain with Megatron. Skywarp became Cyclonus, Thundercracker became Scourge and the rest became Scourge's Sweeps.
Back on Cybertron, when Soundwave retrieves Laserbeak, he doesn't push the eject button on his shoulder to open or close his cassette door. This is not only inconsistent with previous episodes, but also with scenes later in the movie.
After getting a new spacecraft from Quintessa, Hot Rod, Kup, Wheelie and the Dinobots fly over to the planet of junk to meet up with the other autobots. However, they had crashed on Quintessa earlier whilst the other autobots flew onwards to the planet of junk, and seeing as they hadn't contacted them at all since the crash, how could Hot Rods group possibly know which planet the others were currently on?
It is unexplainable how Laserbeak managed to get video recording of the Autobots from all those angles we see when he plays the recording back, considering he was stationary during the recording process. Some of his shots indicate that he moved right in front of the faces of the Autobots, which would have been impossible for him to do, partly because he was outside of their base and partly because the Autobots would have noticed him.
Unicron obviously has his own center of gravity. Galvatron tumbles into Unicron's insides after Unicron swallows him; the robots on the conveyor fall into the processing vat; the Autobots are able to transform and roll out while inside Unicron. If this is the case, though, then considering how much Unicron is moving about during his assault on Cybertron, why aren't the Transformers inside of him experiencing the equivalent of a constant earthquake?
After transforming into robot mode to gun down the Decepticons, Optimus Prime is propelled upward by "jets" coming out of his sides. It is not entirely clear how this happens, considering he cannot fly.
As Unicron is about to devour the first planet at the start of the film, there's a shot of a robot looking up towards him saying "it's Unicron!", at this part there's an animation error. If you look carefully the bottom part of Unicrons outer ring overlaps an object that is in the foreground, this would mean that Unicron is actually smaller than the objects on the surface of the planet and not bigger than the planet overall as established by the next few shots.
As Soundwave carries the damaged body of Megatron through the battlefield towards Astrotrain, followed closely by Rumble carrying Megatron's cannon, they appear to be running in thin air, as no ground is painted beneath their feet.
In the scene where Blaster ejects his tapes, he first ejects what looks like Eject. He stays blue up until he gets to the edge of the screen. He then turns black like Rewind. Then Blaster ejects a another blue cassette, which after about a second, turns black. This one gets through half his transformation colored black, then turns blue for a split second then turns black again. Then, when the cassettes are fighting each other, Eject runs in from the left and jumps over Perceptor. And then he runs in from the left again to shoot Ravage.
When the Allicons (alligator-like guards of the Quintessons) come out of the water reacting to the appearance of Hot Rod and Kup, there are splashes around their feet even when they are on land. Later, when they transform to attack the newcomers, you can see dark-colored stripes running down their features. These were supposed to mark the line under which darker tones should be applied to make a shadow effect, but no shadow is painted onto them, only the darker stripes remain visible.
Then, as Kup is still holding the turret cannon, Blitzwing fires a purple colored laser bolt, and both Kup and Blitzwing's tank barrel are washed in purple light. But only Blitzwing's tank barrel changes color; the turret it's connected to remains its normal tan color.
As Springer and Arcee flee from the attacking Starscream, there is a spot of battle damage on the floor, on the lower left side of the screen, that isn't moving with the rest of the floor. This damaged area even overlaps the subsequent explosion.
When Ultra Magnus is rallying the Autobots against Unicron, somebody must have accidentally moved one of the animation cels. In this scene, his chest shifts slightly to one side, while his head and arms remain still.
After Galvatron, and the newly created Cyclonus, Scourge, and the Sweeps fly away from Unicron inside their brand new space ship, there is a noticeable black dot on the screen that moves along with the ship. When the ship finally flies out of the screen, the dot also stops in its path.
As Galvatron operates a green button in the cockpit of his ship to release some missiles, there is a grey panel right in front of him with rectangular keys on it. It simply disappears from one frame to the next just as he pushes the green button.
When the Quintesson spaceship is nearing the surface of the Planet of Junk, there is a really well animated shot of it spiraling through the air towards the battlefield, with only one problem: the bottom of the ship is not fully drawn, so you can see a "gap" on the bottom of the screen that changes its shape from frame to frame.
After the Quintesson ship breaks apart, all of the Autobots fall into Unicron's depths except for Hot Rod, who falls onto the side of a gigantic spike jutting out of the side of the tunnel and is knocked out. When Hot Rod regains consciousness and falls off of the spike, the animation isn't lined up with the background, so it looks like Hot Rod's legs disappear when he slips off.
In the close-up shot of Rodimus Prime running towards his companions, the green lighting effect behind him is mismatched; it is shifted a bit to the side, overlapping parts of Rodimus, with some of the background still visible in his other side.
When the Decepticons are killing the Autobots inside the Autobot shuttle, there is one of the common Starscream/Skywarp/Thundercracker miscolors. Megatron transforms into gun mode and Starscream catches him and kills Brawn. When they cut back to the Decepticons, Starscream is in front of the Constructicons without Megatron and is firing one of his arm rifles (this probably should have been Skywarp or Thundercracker). When they cut back to the Decepticons for the third time, Starscream has Megatron again and is finishing off the rest of the Autobots.
Even after the Battle of Autobot City, characters who are supposedly dead continue to appear in crowd shots and battles. Thundercracker and Skywarp can be seen at both Starscream's coronation and flying into Unicron's mouth in the final fight scene.
As Brawn is shot down, Scavenger can be seen in the background and he's carrying his gun in his right hand. When Scavenger fires on Prowl, though, his gun is suddenly in his left hand. Then, after Prowl is gunned down and Ironhide and Ratchet return fire, however, Scavenger's gun is in his right hand again.
When Ironhide and Ratchet are gunned down near the forward section of the shuttle, Ironhide is on Megatron's left (after he faces the front of the shuttle). When Ironhide makes his last ditch effort and grabs Megatron's leg, however, he's suddenly on Megatron's right.
On board Astrotrain, as the healthy Decepticons converge on the injured warriors to toss them into space, the panel in the center of Bombshell's chest is colored grey when it should be yellow. Also in this scene, the red stripes on Soundwave's forearms are missing, and Dirge is once again colored like Ramjet.
As the Decepticons gather around the fallen body of Megatron, we see that they do not in fact appear out of the sides of the screen, but actually "pop" into view a few centimeters away from the screen's edges, and continue to run towards their leader.