I think it's because he is still young? It may turn a darker hue (Brown) when he gets older. If that's not the case, it's genetics, a recessive trait in their family perhaps that comes out once every three generations (=・ω・=). That's what I would think, colorblind readers wouldn't mind that though
Where did the 1st son get the gold eyes from? The Alpha has brown eyes and the Omega has red eyes. The 2nd son has red eyes.