The number of reporters waiting for president Stone near the end of the movie keeps changing from 11 to 16 between shots.
When Toby is taking the pop quiz at the beginning of the film, the questions have little connection to the answers. Question 1, for example, has two parts, both relating to general scientific theory, but Toby answers with a complex mathematical equation.
In the pop quiz, the questions are often nonsensical. Examples: Question 3, starts with explaining the etymology of a word, then presents a mathematical formula, and concludes by presenting multiple choice answers that are only different lengths; Question 4 inquires about the scientific method, then shows another mathematical formula, and finally gives possible answers of different masses. Questions also are repeated, in slightly different forms: the first half of Question 1 is repeated for Question 8, while the second half of Question 1 is repeated for Question 5.
Hamegg is quite surprised that a robot such as Astro would save his life. However, as mentioned earlier in the film, the First Law of Robotics dictates that a robot may not harm a human or allow a human to come to harm, thus a robot such as Astro would be obligated to try and save him. Hamegg is well aware of this Law, as he had just tried to invoke it to save himself.
Just before the movie ends, Dr. Tenma says to Toby "wait, Astro, are your sure you're ready for this?" even though Toby was given the name "Astro" after he fell down to the surface. Even after he returned to the city, Dr. Tenma never even heard anyone refer to him as "Astro."
Astroboy's hair-spikes change position from left to right and vice versa throughout the whole movie.
But then, this is in keeping with the spirit of the original TV series, so it not quite a mistake.
Despite being subjected to incredible stresses of "tractor beams" and multiple direct missile and cannon hits, Astro's ordinary clothes aren't damaged. At worst, they get a little bit dirty.
According to Dr. Tenma, Astro was programmed with all of Toby's memories (which is a crucial part of the plot), but it is never explained where those memories came from. Although it's implied that the memories came from Toby's hair, this isn't possible, because memories are not encoded into DNA.
Before activating the Peacekeeper for the second time, president Stone says that 50 reporters are waiting for him outside. The next scene shows those reporters, and there are fewer than 20 of them.