A claim like that needs supporting evidence. I see no reason why segregation among different members of a single community is natural.
> Why should the state force them to live together?
Because segregation breaks down the social bonds in a community, which is bad for the social fabric, which is bad for the community's ability to live and work together, which results in the breakdown of that community.
https://www.bloomberg.com/news/articles/2013-05-03/why-segre...
> And why should the state tell you where to live? Why should the state be involved in your private life at all?
The state does not exist in Libertarian theory. The state already has numerous rules about your private life. You could make the same arguments against zoning and building codes.
Considering that in-group-out-group psychology has been humanity's evolutionary default for tens if not hundreds of thousands of years, I'd say the burden of evidence is on anyone claiming the contrary.
Maybe some groups of people don't want to live together with other groups of people? Different people living in different parts of the city is just natural evolution.
Why should the state force them to live together?
And why should the state tell you where to live? Why should the state be involved in your private life at all?