Since March I've been reading the Divergent books (I started the third one about two weeks ago). I recently watched the first movie for the first time, and about halfway through, when Tris visits Erudite headquarters and speaks with Jeanine Matthews, I started paying attention to the actresses' eye colors.
Because it's in Erudite headquarters where there's a lot of blue (blue is the Erudite's color), Jeanine's blue eyes really stand out:
Her eye color tacitly indicates her undying loyalty to Erudite. It sort of connects to the old saying "the eyes are the window to the soul." She's Erudite to the core, and her eyes demonstrate this.
I'm not quite sure about this, but it seems that Tris' eyes are hazel, a mix of colors:
In a way, this too indicates her faction, or rather her aptitude for multiple factions. Just as her eye color is a mix, she has qualities of three different factions - Abnegation, Erudite, and Dauntless.