Question: How is it that Thomas can understand what the rabbits are saying as shown in the make-up scene and no other human can?
Answer: The humans can actually understand the rabbits. Because notice during the scene when Peter is about to put the carrot in the Old Mr. McGregor's pants, the rabbits are talking quietly, most likely so Mr. McGregor doesn't hear them. And then there aren't any other scenes where they talk at a normal volume, or talk at all around humans, except for at the end when Peter is apologizing to the young Mr. McGregor.
Question: How did Pooh know the guy he met in the park was Christopher Robin?
Answer: Since Christopher Robin is his only human friend, Pooh naturally assumed it was him. True friends always find each other no matter how much time has passed.
Question: How come Miles could venom strike and turn invisible on command just because of what Jeff said?
Answer: Miles was touched by what Jeff said, and it inspired him to finally find the focus needed to control his powers.
Question: Evelyn in this movie immediately struck me as looking exactly like Roxanne from Megamind. Seriously, look at each character. Is there some sort of hidden connection between them? Or is this purely coincidence that Evelyn and Roxanne look like twin sisters? Or... possibly Roxanne being a descendant of Megamind considering Incredibles 2 is set in the past.
Answer: I think the fact that Evelyn from Incredibles 2 and Roxanne from Megamind bear some similarities is purely coincidental. The idea that there may be a hidden connection between the two is unlikely and the idea of them being related is even more unlikely. It should be noted that Incredibles 2 is a Pixar production, and Megamind is a Dreamworks production, so the two aren't even made by the same company. Perhaps, her design was inspired by some features of Roxanne, but the idea of the two being connected or related is pretty doubtful.
Answer: It seems to just be a coincidence, or more likely the limitations of the 3D animation style used. Of course, in real life there are unrelated people who look-alike. However, it's unlikely the characters are suppose to be related since "Megamind" was created by DreamWorks, which is a subsidiary of Universal, which is a division of NBCUniversal (formed by the merger of GE's NBC and Vivendi Universal). Since 2011, NBCUniversal has been controlled by Comcast until they owned it outright in 2013. "The Incredibles" films were created by Pixar, which is a subsidiary of Walt Disney Studios, which is owned by The Walt Disney Company. Plus, I don't think there's been any significant individual who worked with both animation studios who would have influence on the character development and hundreds of people are involved in the animation processes.
Answer: It's not clear if he actually can hear them or not. It's implied in the film that it's possibly stress or a mental break that is causing him to hallucinate their voices, or is suddenly thinking on a brain wave length that can understand them. If it's the former, it's coincidence that he hears similar to what Peter is actually saying. Either case explains why he suddenly can hear them when nobody else can around them despite them talking in front of people.
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