Deliberate mistake: When Metro Man flies towards the observatory to save Roxanne, we see a typical "the-characters-see-what-the-audience-sees" shot - a Super-Man-esque shot of him with his arms stretched out in front of him with his fists clenched. This shot is then projected onto a monitor that Minion is watching. It would be impossible to achieve this. It's as if there's some sort of camera on top of the observatory filming Metro Man, which there isn't. We see the observatory enough times to see that there isn't, and even if there was, the angle at which it would need to be at would be impossible to achieve. The shot of Metro Man on the monitor is positioned right in front of him, panning backwards. A camera would need to be very long to achieve this kind of shot, but there simply isn't one present.
Deliberate mistake: Regarding one of Megamind's lines when he is speaking in front of the citizens of Metro City after having supposedly defeated Metro Man: "Imagine the most horrible, terrifying, evil thing you can possibly you can think of... and multiply it by six." In the Swedish dub, the 'six' is substituted with a 'five' [most likely due to 'six' and 'sex' in Swedish having the same spelling and pronunciation, and wanting to avoid any unintentional sexual innuendos]. (00:22:10)
Answer: The characters are only 'disposed of' so that they won't be able to reveal Megamind's deception. Remember, the warden wasn't killed and neither was Megamind when the warden was transformed into him. It is not necessary for the device to function that the individual being copied be eliminated.
Phixius ★