I recently played through a game where I got four cities to level five.  On the turn that each of them reached 1000 citizens and leveled up the population of them suddenly dropped to 500 then slowly started growing from that point again.  They all reached level 5 at different times.

I am also seeing a problem that when the cities get to level five the number of options I have for city upgrades is so large it goes off the top of the screen and many of the icons cannot be seen or clicked on because of this. 

When demolishing a building that had been placed on a resource tile, (fertile land, mine, etc) the resource that had once been on the tile dissapears.  It is not invisible but still there as I suspected because the same improvement cannot be rebuilt on it afterwards, and there is no indication that it is there anymore when you mouse over it/click on it.

Some new games will spawn the recruitable champions on the little islands on the edges of the map making it pointless to recruit them.

When you attempt to build on a resource with a pioneer and do not have the resources to do so, the game does not tell you what the resources required are so you know when to try again.  This is probably not a bug, but it would be nice if it showed what you were missing.

It doesn't seem clear which mines a forge's 2X iron production effects when many of the mines are pioneer produced rather than part of the city.

This is just an opinion, but the bonuses that you receive for building on the unique tiles in the game, (oasis, scenic view, gemstones, gold deposit, etc) don't really seem worth spending four city tiles on when there are buildings that give you much more productivity for the space taken up.