It was certainly a result of the Al Bhed DNA mixing with the Bevellian DNA. Heterochromia Iridium (having two differently coloured eyes) happens most often when distant genetic lines are mixed. Considering that the Bevellians and Al Bhed had been pretty seperate for about 1000 years, that would be our explanation.


As for this "error" in-game, it's the overlapping of various light. There's no error.