I was wondering why you said this, since I don't think it's neck is too short, but from later posts it appears you do, so the answer is obviously, "Because God made it wrong."
it's = its
It doesn't. A giraffe is a giraffe. Maybe God wanted a giraffe with a neck too short, maybe He didn't. Neither you nor I can ever know that. Now I can live with that but you can't. Being a methodological naturlist I assume, you should be able to offer some explanation for why the giraffes neck is too long, too short or just right. Choose your medicine and give it a shot.