I know from Skyrim that Autosaves, Save on Fast Travel etc can cause issues this is why Autosave, Quicksave, And Save On Fast travel are not full saves they do not save all the scripted info like the normal Save does I have been disabling those since Skyrim they are good for quick and dirty saving say like in the Mechanist Lair where you might CTD from time to time but I always do a normal Save and always load from a normal Save never from an auto save the others just corrupt to darn easily.