I suspected as much just from the fact that after reloading a bunch of times the game starts to really bog down, or hitting Ctrl-N a couple dozen times (trying to get a specific champion in a decent start) starts to break the game with parts of the graphics ceasing to show up (like tile yields), but I just ran into a situation that I believe confirms my suspicions.

I was playing a game and doing pretty well for a change when I got the Spider Queen world event which caused two nests to spawn next to two of my cities, one of them was "Deadly" and promptly razed a city I had just finished a wonder in with no chance of me being able to defeat it for a very long time (400 HP, 300 attack, I had just unlocked shortbows). I loaded an auto-save from a few turns earlier, the event did not pop this time, I continued on as normal. About a dozen turns later I finished building something in one of those two cities and magically an undefended spider nest popped in the same place it had popped before, I collected the loot then a couple turns later finished building something in the other city and the other nest showed up, though again without the spiders. I'm guessing when I reloaded those nests weren't properly cleared from the world and when I finished building something in those cities that forced an update which somehow pulled them from the abyss back into the world.