In certain episodes, you can see that the female character Thunderblast (named Chromia in the original anime) actually has breasts under her chest-plate, as well as clearly noticeable nipples. In one episode, they even bounce around as she runs. This must have been a hidden joke on the animators' part, but at times, the character bends in ways that make them visible.
The original series from Japan was initially meant to act as a sequel to the previous series, Transformers: Energon (2004) (AKA Transformers: Energon), but during production, it was re-imagined as a completely new storyline unrelated to any prior series. When they translated it to English, they reattempted to portray it as a sequel, which explains some of the inconsistencies between it and Transformers: Energon. Years later, the Japanese adopted the American continuity, so now even they consider it a sequel, despite that their version is even more inconsistent with it than the English dub.
It was believed by many that the character of Override was originally created male, and then changed to female for the American dub, to give the show more female characters. (An occasional occurrence, such as in the original "Mighty Morphin' Power Rangers" series.) This was incorrect, as the character of Override was created by the American company and intended to be a female, but shifted to be male in the Japanese version; clues to the character's original gender include her behavior towards Megatron (blushing and acting coy).
Scott McNeil has once commented that had he known that he would be voicing the character called Snarl throughout the show, he would have given him a more unique voice rather than a slightly altered Dinobot rehash, referring to his famous role as Dinobot from Beast Wars: Transformers (1996).
The Autobot character, Crosswise, is accidentally referred to as "Smokescreen." This is probably because of a figure that was named Smokescreen. The figure used Crosswise's body, but had a different paint job. Luckily, this mistake happened rarely and was fixed in later episodes.
Certain characters have unique cyber planet keys, or force chips as they are called in the Japanese version of the show, "Galaxy Force." Optimus Prime's cyber key strongly resembles the Matrix of Leadership, and Megatron's cyber key has aspects from the Decepticon symbol. Vector Prime's cyber key resembles a gear from a clock, most likely symbolizing his powers over space and time.
Most of the characters in the series have cyber planet keys with silver outlinings. However, the planet leaders have cyber keys with gold outlinings. These characters are Evac (the Earth leader), Override (the speed planet leader), Scourge (the jungle planet leader), and Metroplex (the giant planet leader).
The trivia item below may give away important plot points.
In addition to rewriting part of the story in an effort to present it as a sequel to the previous Transformers series, the American dubbing also offered numerous explanations to events that were not or only vaguely explained in the Japanese original. For example, in the original series, characters often received power due to sheer strength of will, and Megatron's return after his death was given no explanation either. The American version often attributed some of these miraculous happenings to the power of Unicron, Primus or the Omega Lock or Cyber Planet Keys.