I noticed that taking unconscious and dead aliens and their equipment onto your helicopter and aborting the mission with all of their stuff in your soldiers inventories corrupts your game save for reason. The game will continue on like nothing is wrong, but if you try to save and then load that save at any point after it will crash the entire game. At least that's what has happened every time I try to do it. If I leave the alien bodies and gear on the battlefield and abort the mission the saves work perfectly again. It happened when I tried to take a medium UFO that had landed undamaged, and then ran into some new aliens and a sniper. All I did was bring one dead, one alive, a new sniper, a pistol, and the clips for them. I can research the new stuff and progress normally but it ruins all the saves after that kinda making it all moot.
Edit: Okay, I figured out it was the just bodies that was crashing the game on save/load. Taking the equipment by itself actually crashed my game on my first save but the autosave still saved properly regardless and loaded okay afterwards and every time after that.