The first one is when Danny is fighting Skulktech(Skulker and Technus combined from 10 years in the future). After they short out Danny's powers, he falls. Watch closely, when we're watching him fall from aerial view, his eyes are green for a split second.

Near the end of the movie, Danny is fighting Dan. After Danny blasts his evil future ocunterpart with his Ghost Wail, Danny is weakened and turns human. Then when Dan recovers, we see a close-up of Danny's face when he says "Time's up" his face is cut and bruised, and his hair is in his face. His eyes are green, and his hair is white although he just changed back to human.