From what I have seen, there are 3 possible options.
Branch has depression, and though he has good days, he often has bad days, as many who suffer from depression never fully get rid of it, it just kinda... goes away for a moment and lingers quietly till it's ready to take hold again.
(and please know I got this from a video theory on Youtube. They do much better explaining it and supporting the idea)
Branch is a Hybrid, or rather isnt fully Pop troll. And the more he sings pop songs or acts like a pop troll singing and being happy, the more color he has.
The person who's video I watched pointed out that Branch has more pointed ears then most pop trolls, more like a rock troll who seem to be more gray/black in color. And as we never see Branch's parents in the original movie only his nan who passes away when he was young, it is a open possibility.
and Three, probably most boring answer:
The people in charge of the movie thought kids are stupid and figured they would not be able to identify Branch if they changed his color too much from how he originally was in the first movie.
OR they found gray/black materials for toys much cheaper and made the movie makers go with that.