There's numerous bugs with loading games. Apparently a lot of things still aren't being saved and loaded correctly so reviewing that process would go a long way.
One of the main things that bothers me is the fog of war seems to get messed up. Resources and stuff you've found before don't show up anymore unless you send a unit there again.
Also strategic map yield display seems to work randomly. Sometimes I have to exit the game and reopen a new instance to get things to display correctly. Makes it very hard to determine where I want to settle.
Another one is it sometimes messes up quests. I know I should have saved games for these but I'm at work right now. Anyways sometimes when you start a quest and then save. And then go to the destination and complete or fail it then reload the previous save because you didn't like the result or whatever, the quest won't be available. Some flag must have not gotten cleared or not reset properly because even in the reloaded game where the user hasn't gone to the destination yet it appears as if you did already. Sometimes you'll see the monster army related to that quest roaming around.