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.
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 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.
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).
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.
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.
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 suppose to be 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.
In one scenes, 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.
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.
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.
Noah discusses his plan to destroy the transwarp key while riding inside Stratosphere. Stratosphere should have been able to hear his plans.