I have two strange bugs in my current game. I do not know how either occurred.
I took over an enemy city, and in the center of it, right on the hub building, is an earth mana shard. You cannot build the structure to harvest it. I do not know how the AI managed to build a city on top of a resource. The city is Chi'laa.
The second is even more odd. One of my heroes was apparently incapacitated after a battle. He died in the battle, but his army wasn't defeated. To my surprise, I noticed the army had the incapacitated X over it, and only that hero (Arcturus) cannot move. I didn't think much of it, until I noticed I had a unit stationed in a nearby city suddenly. It is Arcturus. Apparently when he died and was incapacitated, he was sent to the nearest city as usual, but since his army wasn't defeated, he never left the army. So now I have two Arcturus's. His double is in the city of So'laa. Oddly enough, the big X over Arcturus's army doesn't got away, even after he can move again.
Here is the save game, if that helps. https://www.dropbox.com/s/h3fe96caxn1saz5/Prot.EleSav