Well, there's no other way to better explain this, other than by flat out saying that Rachel's eyes were NOT green at all.
When Deckard confronts the replica of his former lover, he is immediately overwhelmed. He shares a silent intimate moment with her, and then immediately ruins the moment by blurting out "her eyes were green", and turning away.
Well, my first guess is that his memory of Rachel might've been impaired due to how long it has been since he saw her, and also due to the fact that his prolonged isolation might have cause mental deteriorations. But these seem very improbable.
So to restate the question : Why exactly does he say that? Am I missing some important detail, because this specific line had caught me off-guard.