When Minion confronts Megamind about dating Roxanne Ritchie, Megamind disables Minion's arm. When Megamind says maybe he doesn't want to be the bad guy anymore, Minion recoils with a gasp and lifts both arms in surprise which he shouldn't have been able to do with a disabled arm. Minion is then shown driving away on his Segway, and his arm is once again disabled.
When Megamind, disguised as Bernard, is in the library with Roxanne, the book he reads before the next scene is titled 'Megamind Unmasked'. The back of the book is actually a summary of a different book, 'The Happiest Me I Can Be' which is a book not seen until later into the movie.
The goof items below may give away important plot points.
When Megamind dehydrates Bernard and then assumes Bernard's likeness as his disguise, he scoops up Bernard's eyeglasses and cellphone from the sky-walk. In the credits extra scene, when Bernard pops up out of the washing machine after being re-hydrated, his glasses are askew on his face.
When someone disguises as another through the watch, the person is physically similar to the impersonated one, with exception of the eyes. This is seen when Megamind impersonates as the Warden, Metro Man and Bernard. But at the end, when Minion impersonates Megamind, his eyes remain green, when they should be brown, as Minion's are.
When Megamind transforms into different forms, his voice changes to match the character. However, when Megamind transforms into Bernard, his voice remains that of Megamind's. This is explained though as we see the watch recording the warden's voice during Megamind's escape from prison. He didn't get the chance to record Bernard's voice in the rush to replace him in the museum and had to use his own voice.
Megamind seems to be a free man at the end of the movie. Although he became a "hero" for defeating Tighten, the legal system should have remembered that he created Tighten in the first place. Also, there were numerous life sentences he was already serving, plus he is never charged with the murder of Metro Man (who is still believed to be killed by him, even though we know better). It's unlikely that a single good deed would merit a full pardon for his entire career of crime.