I've been using (read: abusing) manual improvement placement in this particular playthrough to stretch & snake cities, partially to reach for resources, and partially to reach out and touch terrain in order to block the AI from moving past choke points. It has lead to some interesting issues with cities crowding very close together. One city in particular has been very badly behaved. I'm unsure if this is caused by my manual placement chicanery, or something utterly unrelated, but I managed to place a market completely mis-aligned from the standard improvement grid for a city.

You'll see it here, right next to the bees and scrying pool.

It's also mis-algined in 3D mode.

Additionally, this city has problems simply placing improvements at all sometimes. There's plenty of room, it just doesn't want to actually put them down. I dont know if it's my shenanigans with extreme snaking, the very late game state of this particular game in general, or what, but there's some weird things going on up in this bitch.

Save game for your enjoyment.

https://www.dropbox.com/s/br4fg89ph2e5p6y/Broken%20Market.EleSav