I am with my friend now, and he says that The Bunker is already a good movie in comparison... Heck! There are explosions! And war!
He recalled some more detail about the plot, the Nazi put the sons against the fathers in some way.
A secret society "reprogrammed" children to kill their parents.
EDIT: seeing the clip actually unstuck his memory! The movie is
Los Sin Nombre [1999]. Thanks!