There seems to be an issue with the order and timing of processing events, both player initiated and AI initiated. When an event happens, like being attacked by the AI, or auto resolving a battle, the UI should focus on that event and not jump to something else until the first event is completely resolved. Here are some examples of what I mean.
When you click auto resolve on a battle, the map jumps to the next available unit. Meanwhile, back at the battlefield, a cute little animation is playing with one unit (hopefully yours) defeating the other unit, but you don't see it because the game figures that you should go do something else now. So you start to think about what to do with this new unit, and suddenly you get a window with the auto resolved battle results. It should go auto resolve, animation, results, next unit, not auto resolve, next unit, animation, results.
This one is annoying because it can currently result in you researching nothing until you figure out what has happened. You end your turn and some AI unit decides to attack you on their turn. The problem is, your turn "starts" before you find out you were attacked, and if you researched something this turn, you get the research screen before the battle from the AI's last turn starts. So the research screen pops up, and then you find yourself in a battle. At the end of the battle, all the windows are closed and you didn't select a new research objective. Again, it should deal with all of the events from last turn before it starts doing anything for this turn.
I also seem to recall nervously ending my turn next to an enemy. When my turn started, I quickly moved my units out of harm's way. Then I get a message that I am being attacked. What? They aren't there anymore! Again, things are happening out of sequence.
I imagine that this is a result of the wonderful multi-threading that makes our lives so much easier.