There was a scene after the Parr family escapes imprisonment with Violet's help, near the end of the movie, in which we see a van full of bad guys. They celebrate while Syndrome impersonates a Super and causes havoc, but not long afterward Mr. Incredible ruins the party by entering that van and closing the door, so viewers can't see what happens inside.
When I was a kid, I thought that he simply knocked them out, but now I remember that he killed some other bad guys throughout the movie. I don't mind superheroes killing their enemies, but I'm curious as to the implication behind that particular scene. Word of god would be appreciated, but I doubt there is one.
Did Mr. Incredible actually kill those henchmen?