Both the original English TV and later DVD versions of the first episode had several dubbing errors. The DVD dub inserted an argument between Kicker and Misha that can be heard over the sequence of Ocean City rising from the water. This addition doesn't make any sense, because Misha isn't in the city. The original TV version instead had Demolishor monologuing to himself about the changes that took place since the previous series. In both versions, Sally's mother says a line in Sally's voice. In the TV version, the dialogue between Dr. Jones and Rad, as the Autobots leave for Mars, is out of sync with their lips. In the DVD version, Optimus says that 20 years have passed since the previous series, instead of 10. In the TV dub, Alpha Q is said to be a servant of Unicron. Later episodes would reveal that this is very far from the truth. This line was deleted for the DVD release.
English version: The Energon Sword is said to be Megatron's Star Saber. Both of these are incorrect: the sword has nothing to do with the Star Saber and it didn't belong to Megatron either. Instead, it was created from his body and Spark.
In the original Japanese version, Demolishor tells Cyclonus a rumor that Megatron has returned. In the English dub, Cyclonus is the one who tells Demolishor that Scorponok has returned, even though neither of them know who Scorponok is.
The English dub of the series often took figures of speech literally, which lead to a great number of nonsensical lines in the script. For example, when Rodimus is first described, they originally say that he has gone forward towards the future. In the dub, however, this is mistranslated to suggest that he has time-traveled into the future.
The English backstory of the Omnicons is mangled by translation errors. For example, the dialogue inserts a mention of Megatron, making it seem like he had been one of the Transformers to form peace - in reality, the Omnicons are Transformers who have left their home planet ages ago, whereas Megatron stayed behind. It is also claimed that these peaceful robots became today's Transformers, which is again incorrect: they became the Omnibots, separate from all the other Transformers.
In the episode "Go for Unicron!", when Rodimus is about to save Scorponok. When Landmine and Prowl are at the top of the metal hill, you see that Landmine is not in supermode/brute mode. After they get hit by the shot, Landmine is flipping in his brute mode.
In the episode, "A Heroic Battle", when all the Autobot's form up in front of the Energon Grid, you see Roadblock, and Hot-Shot in their uncombined forms, but in their next shot, they are in their combined forms.
In the episode, "Improsoned Inferno", Cliffjumper's and Downshift's names are mixed up. This goof is fixed in Episode, "Omega Supreme". However the error returns in later episodes, and the names of said characters constantly keep changing.
In the American dub, the title cards of the episodes "Scorponok", "Imprisoned Inferno", "A Tale of Two Heroes" and "Decepticon Army" are misspelled as "Scorpinok", "Improsoned Inferno" "A Tale of Two Heros" and "Deception Army". Only two ("Imprisoned Inferno" and "A Tale of Two Heroes") were corrected for the DVD release.
Wingsaber is hellbent on capturing Shockblast who has killed his friend, and he does manage to do that. But when Shockblast escapes, Wignsaber, for reasons unclear, doesn't care anymore and doesn't go after him.
English version: All throughout the series, it is never explained why Megatron, who has formerly died as Galvatron, goes back to calling himself by his original name after he is resurrected. This is actually because in the original Japanese version, he never renamed himself to Galvatron.
Optimus and Rodimus decide to put their differences (on whether Unicron should be destroyed or not) aside but only to fight against Galvatron. Despite being an important matter, their argument is absolutely forgotten after this happens, and they are never shown resolving it. Rodimus simply begins following Optimus without explanation.
English version: In multiple episodes, the fact that Unicron's head has turned into a miniature star and that the dots floating around it are meant to be the "sparks" of Alpha Q's former planets, is left entirely unexplained, even though this is the main point of the entire story. Between the badly translated English dialogue and choppily edited shots of the original Japanese version, it is nearly impossible to tell what is going on in several episodes.
Several times, especially during the first episodes, the lines around the CGI characters appear to be immensely thick due to rescaling errors, which makes it near impossible to see just what they are doing.