Re: Contradictions between Firefly series & Serenity
The comic 'Those Left Behind' gives a pretty concrete explanation for the backslide in Mal's character from the end of the series ('Objects in Space') to the events of the movie.
The only real contradiction between the film and the series is Simon's involvement in River's rescue from the Academy, but the most logical reason for why it was changed is that it makes her rescue more dramatic and relatable to the audience if her brother had a hand in it directly.
Starbuck: We're all friendlies. So, let's just... be friendly.
"Ze director's cut is ze film you saw in ze theater."