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.
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 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.
The goof item below may give away important plot points.
In hailing Megamind as a hero for defeating Titan, no one seems to care that Megamind created Titan in the first place, nor is he held responsible for the crimes he committed while he ruled the city, or for the dozens of life sentences he was already serving, or for, as far anyone knows, murdering Metro Man.