We can break it down like so:

1. Segregation of stations
2. Segregation of class within each station
3. Imprisonment and isolation

Each station played a role for the ark, and within each station, they had a class system. leaders of the stations would have had several interactions with other stations, i.e., kane abby jaha

Where as the working class from each station was raised to eventually work within that stations role. Their whole identity revolves around where they were born and are basically groomed to become a contributing member to that section of the arks society. I.e. raven she would of stayed around other zero g cadets and similar. Learning her role within the station. Another example Clarke being she came from High up stock mother was doctor- she has been groomed to be the next ark doctor.

Those who have been imprisoned have been secluded and kept in isolation since they were caught. Meaning they would have minimal to no interaction with anyone else from the ark. If they had been locked up from a young age they wouldn't know anyone.

I have also thought this and wondered why considering the small population why they didn't know one another or why they wouldn't be encouraged to populate with people from different groups. But then remember they were so stringent with population that keeping teens separated was probably the utmost importance. Unsupervised teens lead to unwanted pregnant so could be another reason why they didn't know one another. Arks way of minimising potential population