I was at war with an AI and found when i went to attack their city, it was just a plain tile with no buildings on it, there were districts around it, but no main settlement. There was no problem with besieging or any mechanic, i think it is just a grapchical bug, but it appears to be on quite a few of the outposts/cities i have encountered other than mine.

Here is a screenshot of what it looks like.