I happened to notice a few articles out there quoting the hair colourist for BD.
Based on her comments, it does look like there was intentional, although slight, darkening of Bella's hair at the end, which will continue in the next movie. Rob looks like his was darkened up too to match up better with Kristen.
"Her hair needed to have depth and warmth and stay in the warm, reddish brown tones, but it needed to have shine and vibrancy. There will be a slight change in the last Breaking Dawn film but I need to keep that a secret!"
"We kept his colour close to some of the other films but it had to be a little deeper this time. You will see why when the next film comes out."
“Originally, he was going to try and get away with not coloring his hair. I believe in the first film, that is his natural hair color. He just felt like if I don’t have to do it, let’s not. In general, men’s hair color is very natural looking, so even when you color men’s hair, you want it looking really natural — like a man. [For Breaking Dawn,] it had to be richer tones, more along the lines of Bella so they looked right together.”
"It will take an amazing amount of control,” she mused. “More even than Carlisle has. He may be just strong enough…the only thing he’s not strong enough to do is stay away from her. That’s a lost cause.”