In Blade Runner 2049, why does Deckard say Rachel had green eyes?

By saying that Rachael's eyes were green (although he knew perfectly well that they weren't) he basically told Wallace that no, Wallace's attempt to bribe/psychological torture will not work on him and that he wasn't just programmed to fall for Rachael as soon as he sees her.

I asked myself the same question: "So, if Wallace didn't make such stupid mistake with the eye color, would it work? Would he make Deckard cooperate?", but then I realized Wallace must have had access to Rachael's DNA (from the bones and hair) and wouldn't make such mistake, and then I checked with the original that Rachael's eyes weren't green, and this brought me to the conclusion above.

He's saying it because he realizes that she is a copy of Rachel, not the real Rachel. No matter how hard they resemble each other, it's not her. Even if the eyes match, he would have found something else that reminds him that they are not the same.

In saying so he knows that the (copy of) the woman he loved will be destroyed. This shows that he puts the safety of his daughter above anything else.

And it's a jab at Wallace's Hubris. He may think he's a god but he can't duplicate Rachel.

Because Rachael did have green eyes although Sean Young does not.*

^{* - This was a continuity error. There is a later scene where we see Rachael with Sean Young's natural brown eyes.}

During the Voight-Kampff test this can be seen pretty clearly.

Because having them create another Rachel was like a punch to his gut, and their ploy to unnerve and unbalance him, while gaining emotional leverage, was working.

Since he's the only one who knew what the original Rachel was like, in person, by making them think, perhaps, that they made a very fundamental error that rendered their attempts at manipulation to be a transparent failure, they'd give up on pursuing that line of action before they could fully succeed in breaking him.

It was a strategic and defensive lie on his part.

The answers about Deckert expressing contempt at Wallace's attempt to influence him are good. That's really why he found fault with the new Rachael.

As a side note, I just wanted to mention that some people with brown eyes can appear to have green (more accurately, olive green) eyes when bright light shines on them from the side. On rare occasion, I've had people say my eyes were green while out in daylight when clearly my eyes are dark brown in any other kind of light.

So this might explain why Rachael's eyes appear to be green in the scene with the Voight-Kampff test in the original Bladerunner movie. Although it wasn't her eye projected onto the machine's screen, in the footage just ahead of the test Young's eyes do appear to have this faded green effect as the light shines on her face from the side. That's shortly after she mentions the owl and as Tyrell enters the scene in front of her.

The director, the writer, or Ridley is poking fun at the gaffe in the original Blade Runner where Sean Young's brown eyes are erroneously shown to be green in the VK test. But this also works as a clever plot element in 2049 as a superficial reason for Deckard to reject this copy of Rachael and to show Wallace that he cannot be bought - even with this greatest gift Wallace can offer him.