Bumblebee's sneaking off to Griffin Rock to track down a fallen meteor seems very out of character for the Bumblebee of Transformers: Prime. Until you realize that the real reason he went after the meteor was that he probably wanted to collect a piece for Raf.
The mission is actually diplomatic. At the rate things are progressing on Transformers: Prime, the Autobots will need to establish a public alliance with Earth soon, and that will be a lot easier if they can demonstrate that Autobots have already lived peacefully among humans and saved their lives.
Out of all the Bots, caveman Ira is very close to Boulder in particular. It's later revealed that the Autobot who saved Ira was Salvage, who looks similar to Boulder.
Blades' situation when you think about it. He's terrified of heights and yet everyone expects him to spent the rest of his life flying as a job. And to make matters worse, it's never investigated if it's possible for him to change forms.
Dr. Morocco and his mechanical chamber of eternal youth. Just who knows how long he can keep using that thing after a whole century of staying young. But the machine has an adverse effect: Whenever Morocco uses the machine to regain his youth, he rapidly ages and has to use the machine very often as a result. There is Paranoia Fuel for the thought of the machine eventually malfunctioning or even Morocco aging too fast and does not make it to the machine on time.
Though given his actions it would be hard to feel sorry for him should that ever happen.
In "The Last of Morocco" Jules Verne wipes Morocco's memory so he returns to being the good person he was back when they were friends. Seems like a happy ending at first, until it sinks in that the reformed Morocco is still rapidly aging and dependent on the youth chamber.
Speaking of Dr. Morocco, when Dither was left behind in 1939, which caused Morocco to rule the town with an army of Morbots but it never details about state of the outside world or how exactly Dr. Morocco took over or how long he has been ruling. If Dither allowed Morocco to build hyper advanced shape-shifting killer robots potentially as early as the early 1940's, it is highly unlikely he would ever kept all but the best of his new tech to himself and any potential clients would be pretty nasty people themselves. And who exactly do we know is active during this time-frame yet will never be allowed to appear or be mentioned in a show for very young children?
Related; most of the characters in the Bad Present have reasonable (if depressing) explanations for their altered roles or absence. Doc Green never came to Griffin Rock because Morocco wouldn't have wanted competition, neatly explaining where he is and probably where alternate Frankie is if she exists. Chief Burns never became police chief because A) he wasn't necessary and B) he's too moral to suit Morocco. Kade, Graham and Dani never had the exposure that would have inspired the career paths they have in the normal timeline and even if Graham wanted to become a proper engineer, the family couldn't afford it. But then we get to Cody...who outright was never born! That in and of itself is already nightmare-inducing but then you realize the most likely explanation for "I don't have a son named Cody" is either "Chief Burns' wife was killed before she could get pregnant with a fourth child" or even worse, "she was killed during her fourth pregnancy"!
When the team finds Professor Baranova in her lab, she mistakes them for hallucinations at first, implying she had been experiencing hallucinations for a while after being alone for so long.
In the Season 4 episode "Mayor May Not", Doc Greene builds a "Molecular Collidor" which we're told later is reaching fusion. After he gets locked out of the lab, we're told that if he can't get to it soon enough, there'll be an explosion capable of destroying the entire island. So, basically, he just (inadvertently?) built a freaking hydrogen bomb, that apparently doesn't require an atomic (uranium/plutonium) trigger, that's about the size of a loaf of bread. Horrifying whether he knew a fusion reaction was possible, and failed to put in safeguards to prevent it, or if he didn't realize that his gadget could reach a fusion state.
This show takes place on Earth, in the same continuity as Transformers: Prime. In Transformers: Prime, the Earth was Unicron.
