She's magic. Her eye color changes every two days. It's not a skill she had in the manga.
But really, anime-wise, I think it's the animation style, which changes a lot. You may notice that the filler episodes frequently use the aquamarine color, but in the more important episodes and all the movies, it's a very deep forest green (<3), which is probably her true eye color. Also, the manga draws her eyes as jade green, as mentioned above.
There's a lot of variation in CCS's animation styles. I guess it depends on the artists and exactly who it is that's drawing. It's not like the CLAMP artists alone drew all 2,898,000 frames of the show.
