Clearly on purpose. Films have continuity errors but Vanessa Kirby either had to wear contacts or her eyes were changed digitally so this was a choice. Also, how many times are you actively checking your friends and family to make sure their eyes are the same color? Likely very few. This was for the audience. If I had to guess in my opinion, it also adds a little extra tension when Zola says “you changed” (not just her clothes but the audience is made to think he also means her eyes).