X-23 has a tendency to shift eye colors depending on writer or artist depicting her at the time. In the v3 comic alone it switches per story arc almost. Takeda depicting her with the more common and character accurate green eyes, but Noto and others having a tendency to vary between blue, brown, gray, and Hazel.
New X-Men: Academy X itself bounces back and forth between initially blue, then green, and occasionally gray. X-Force v3 tended to stick with the officially accurate green eyes. Avengers Academy leaned on a gray, brown, or hazel color influence. Avengers Arena seems to stick with blue or gray eye colors. Her origin stories portray her with the same green eyes as her mother, cousin and aunt, reflecting it as a family trait(Innocence Lost and Target X). Her appearance in Daken: Dark Wolverine showed blue eyes, but was also during the midst of his own father issues and right after Gambit and Laura had teased him about her origins. Something that was akin and reminiscent of the same verbal abuse Laura took from Dr. Zander Rice at the Facility.
The official eye colors are:
Earth-616 Marvel Universe: Green Eyes
Earth-11052 X-Men Evolution Animated Series Universe: Green Eyes
Earth-10005 Fox X-Men Cinematic Universe: Unknown (Has yet to appear.)
Earth-8096 Marvel Animated Universe (Wolverine &The X-Men): Brown Eyes
Earth-199999 Marvel Cinematic Universe(includes S.H.I.E.L.D. TV series): Unknown (Has yet to appear, and unknown if will)
Disney XD Marvel Universe(No Known Numeric Designation Yet): Unknown (Has yet to appear in Ultimate Spider-man or Avengers Assemble. Unknown on if or when she will.)