I think that the problem causing all of the Autosave issues is that Autosave is not done first when ending the turn.  The order of events should be:
1. Click End Turn.
2. Autosave saves the game.
3. Your turn ends.
4. Other turns happen.

I know that they try to make use of multi-core CPUs by having a bunch of stuff calculating simultaneously.  I think what's happening is that they're trying to do autosave that way, so the save game is being written while things are changing.  That's why when you load an autosave, things aren't the way they were when you ended the turn.

So, the proposed fix is this:  When you click to end the turn, run the autosave, and while it's saving, do absolutely nothing else.  Once the autosave completes, then other stuff can happen.  This may also reduce the number of end-turn crashes, and maybe savegame corruption on autosaves (although I haven't seen that in a while).

Of course, I don't know for certain how it works, but this hypothesis does fit the available facts.  Even if I'm wrong, autosave is broken and needs to be fixed.