I'd imagine this has been reported before, but I'll post it anyways.
Very often you get overlapping events and windows in the game.
For ex, you click to battle something and suddenly the research results window pops up, then the battle screen comes up, you click auto-resolve, pick your tech, then battle results pop up then next tech select pops up and basically what you get are alternating windows for 2 different events that have multiple windows
I've even had 3 events with alternating windows if a battle, spell, and tech all hit at the same time.
Now, I'm a god of computing so other than this being idiotic, I'm able to multi-task and hop between the various windows flying all over the place. But it is kinda silly and I'd imagine it's confusing as hell to newer players and mere mortals.
I'm not sure if this only happens when auto end turn is enabled (which is the game's default that I leave as is).