User blog comment:ArtixBot/Neo's Eyes/@comment-2135507-20140825222945/@comment-2006510-20140825223849

That's sorta because Vol. 1 was known for small errors like this all the time - I never had an issue with it, but it didn't go unnoticed by many

I bet it's fully intentional myself. When her eyes are both brown, she has her arms crossed and a serious expression, even stoic all throughout that meeting - but when her eyes are different colors, she's almost grinning, and bows politely to Team RWBY.

It's not unlikely; Yang's semblance changes her personality (and eye color) a bit after a certain point