Because he was purposely made to look like Scar. It wasn't until far into the production cycle when Disney decided that, due to incest concerns, that Kovu will no longer be Scar's son. However, it was too late to change his character design, so he still looks like Scar, without having any relation to him any more.
I just figured he'd have his own unique character design cause of the many Lions involved in the movie. Not to mention, he was technically on the dark side, so I figured it would be easier for little kids to understand if he was darker, like Scar was.
Technically, Scar isn't brown. He's more of orange. So, that wouldn't completely explain Kovu's color. But it obviously was made to make difference between "two sides". Proof is the fact that lionesses from two sides also looked different.