It's explicitly stated that Scar is not is father. And honestly... the have different body types and fur colors. Kovu looks more like the Asiatic lions of the Night Pride. Here's my theory:
Nuka is Scar's true son. However, when Scar saw how weak and sickly the cub was, he tasked Zira with "creating" a suitable heir. So she traveled... and found either the Night Pride or a rouge Asiatic lion. By the time she returned, Scar had been killed and Simba took the Pridelands back. Then, y'all know the rest. But that is my current theory.
What do y'all think?