Board Thread:General Discussion/@comment-26968099-20160412021110/@comment-26397825-20160412022043

A lot of things became light reactive as they fiddled around with the lighting over the course of the volumes, and eyes are one of those things. Though they tried to fix it wherever they could, it's kind of hard to double check the eyes in every single frame.

So it's literally just the lighting messing with them. Jaune's eyes turn very brown in the cute scene he and Pyrrha have before she starts asking him about destiny and what she should do, and when Ruby says that she's going to go after Jaune and Pyrrha and bring them back to the group at the very end of season 3, her eyes are dark blue instead of silver. Her eyes also had a yellow glow to them when she was talking to Summer's grave right at the very beginning of the show. They're just reflecting the colour of the lights.