The cothon clipping:

Wonder and district models not showing on reloading a game:

I had the same issues. The disappearing bug even happened with armies sometimes. I was still able to select and use them, just that I couldn't see them anymore.

I have also seen the models for Outposts not change and still show as destroyed after my oppenent took one.

Same here. After a battle against other AI units mine turned invisible. 

I guess it's a perk unlocked with experience. Now I can infiltrate and take cities in a whim

>:)