Scourge's grill is decorated with insignias taken from his slain enemies. The insignias are of various factions from Transformers history: Autobot, Decepticon, Maximal, Predacon, Mercenary, Terrorcon, and Wrecker.

During filming in Peru, a Peruvian child showed his Transformers drawings to director Steven Caple Jr., and in response, Caple invited him to the premiere, and paid to renovate his school's roof.

When Scourge taunts Optimus Prime by saying "Primus would be ashamed", this marks the first time that the Transformers' creator god from the 1980s Marvel Comic series, Primus, is mentioned in the live-action movies. According to most versions of Transformers lore, Primus was the ancient rival or brother of the evil Unicron. Both were cosmic beings who battled across different universes, until their souls were trapped in two asteroids that they turned into planets over time. Primus became the planet Cybertron where he created the thirteen Primes, robotic deities who then created the different Transformers types.

According to Steven Caple Jr., Optimus Prime's face in this movie is visually based on his voice actor Peter Cullen.

Most of the film's computer animation was done by the company MPC, rather than ILM who had done most of the special effects in previous Transformers films. Reports suggest they struggled to finish the effects on time, which meant many scenes had to be cut (including a character called Transit, a Decepticon who turned into a bus to hide from Optimus Prime) or altered before release. In November 2022, seven months before the film's release, the animation company Weta Digital was hired to assist MPC and finish the film on time. Most of the ending battle was re-done from scratch by Weta. Early teasers and trailers showcased many of these unfinished effect shots, including the abandoned MPC version of the final battle. The opening scene set on the Maximals' home planet was also a late addition by Weta, and the character Apelinq was thrown in at the last minute. In anonymous correspondence with Transformers fans, certain MPC animators apologized for their sub-par CGI work in the film and admitted that MPC only got the job because they were cheaper than ILM. ILM was also busy working on the film Transformers One (2024).

Continuity

The symbols on Scourge's left arm change a lot throughout the film. For example, the Predacon and Decepticon logos in the beginning of the film change to Maximal and Autobot ones in a later scene. They change back to the Predacon and Decepticon logos during the final battle however.

When on first seeing Elena Wallace, leaving her car with four coffee cups in her holder, by the time she has entered the building and took the stair to her office, she has only three coffee cups in her holder.

When Optimus Prime states he is going to sacrifice himself by destroying the key, Bee takes Elena and drives her to safety. But Elena is not in the car-Bee when Bee is seen next. However, when Bee transforms into his robot-form, he has Elena with him.

When Stratosphere transforms at the Maximal village, he begins facing away from Optimus Prime. When the camera cuts to the other side, Stratosphere has somehow turned completely around while still half-transformation.

When Noah first sees Mirage's robot form in the New York warehouse, Mirage is about twice as tall as Noah. Noah's head reaches up to the middle of Mirage's thighs. Later, in the Peru scenes, Mirage is about four times taller than Noha, whose head only reaches up to the middle of Mirage's shins. Mirage doubled his height between scenes.



Factual errors

All of the establishing shots of the Twin Towers of the World Trade Center in the film show an antenna mast on the top of the South Tower (Tower 2). The actual Twin Towers had its antenna mast on the top of the North Tower (Tower 1).



Incorrectly regarded as goofs

When Noah and Elena open the underground spiral staircase in Cusco, Peru, Noah mentions the staircase looks like something from Indiana Jones. The particular film he is presumably referring to, 'Indiana Jones and the Kingdom of the Crystal Skull', which takes place in the same location and has a similar staircase, did not premiere until 2008, while 'Transformers: Rise of the Beasts' takes place in 1994. This assumes Noah was referring to that specific movie. Indiana Jones and the Last Crusade (1989) came out 5 years before this movie was set and featured a similar spiral staircase built into a floor.



Revealing mistakes

When Stratosphere begins transforming in Peru, the base of his left wing noticeably clips into his fuselage.

When Stratosphere first meets with the others and crash lands, there are a few compositing errors:

He destroys much of the pavement and sends large chunks of debris flying, but the shrubs and bushes he lands on are not disturbed and stay perfectly still. His foot clips into the exploding debris as he sets it down. Rubble flies upward rather than being pushed down by his foot. Grey concrete debris bursts out of the ground from underneath the bushes rather than soil and plant matter. As the debris crashes back down on the shrubs, the plants are still not affected. Bits of rubble on the pavement behind Stratosphere's right foot appear out of nothing, without anything contacting that area. Some of the debris overlaps the base of the tall cylindrical tank next to the warehouse, even though the debris should be behind it.



Miscellaneous

When Noah is talking to Kris in Kris's bedroom after he meets the Autobots, Mirage is standing on top of a car in order to be tall enough to peek into the room from the alley and be at eye level with Kris and Noah. Later in the scene, he does not need to stand on the car to be at eye level with Noah and Kris as they are standing on the fire escape that is the same elevation of Kris's bedroom.

All throughout the film, the way that Optimus Prime's shoulders attach to his body keeps changing. This is because his robot form wasn't designed with realistic shoulder movement in mind, so his arms are just "floating" beside his body. In some shots when he raises his arm, it can briefly be seen that the shoulders' inner side that's supposed to connect his arms to his torso is actually attached to nothing.

When Bumblebee first transforms from a car to a robot at the New York warehouse, the hood of the car with the black stripes recedes into his body. Then, the purely yellow car parts that become his chest shrink, morph into a different shape between frames, and the black stripes reappear on them. A shadow was added over his chest to hide when the black stripes reappear, but these parts noticeably change color when he transforms, and the actual black striped hood piece simply vanishes.



Anachronisms

Kris is playing a Game Boy, claiming he's unable to beat Bowser. The film is set in 1994; none of the Super Mario Bros. games for the Game Boy in existence at the time had Bowser as their villain. Additionally, the sound effects heard are from the NES, not the Game Boy.

When Elena is using the PC, the operating system is Windows 95, which wasn't available until August 1995, but the film is supposed to be 1994.

In one scene, Mirage transforms into a Formula One race car. However, he transforms into a model of the race car that used between 2009 and 2013, even though the film takes place in 1994.

The song "Hypotize", recorded in 1996, by The Notorious B.I.G. plays but was not released until March the 4th 1997 on the Bad Boy and Arista labels.

Noah has a Wu-Tang flag in his bedroom that uses the version of the Wu-Tang logo introduced in 1995, but the movie takes place in 1994.



Audio/visual unsynchronized

After Rhinox runs into Wheeljack and throws him aside, Wheeljack says "Ay-ay-ay!" but his mouth doesn't move.

During the final battle, when Optimus Primal says "We'll clear the way!", the line is spoken by David Sobolov rather than Primal's voice actor Ron Perlman. Sobolov originally recorded preliminary voice work for Primal before the voice track was re-recorded with Perlman, but this line was left as is. Fans often believed the line is said by Rhinox but Rhinox's mouth doesn't move in this shot.



Plot holes

Noah discusses his plan to destroy the transwarp key while riding inside Stratosphere. Stratosphere should have been able to hear his plans.