I have the same problem and find a cause for me. In the combat with stone lord, an enemy heals himself the moment I kill him. I don't know why these two things happens at the same time. Anyway, as a result, the enemy is dead with hp not equal to 0. Since then, every time I leave for another place and go back to lower city, the game crashes. It crashes because of the 'undead body'. It tries to load this bad game object whenever it loads lower city because the object is in the sewage of the lower city. Thus, when I pick the body with me or put it in the camp storage, I can load other places like Iron Throne and head back to lower city. The bug is still there, but by putting it in the bag or in the camp storage, the loading process will avoid it. I guess this works because the camp and bag are loaded into the memory at the first-time u load the save files, which surprisingly won't trigger crash. Throwing it in the ground in ur camp is useless, cuz the camp environment is with the city, which also will be reloaded when u load the city.
This solution may only work for me. But as a reference, I suggest u can find the latest good save file, which can be tested by traveling to Rivington and traveling back to lower city. And check what have u done between the good save file and bad save file. U may also find some bad game object like my 'undead body' there. Then u can go back to ur latest save file and go to move that bad game object into ur camp storage. In this case, u can still play smoothly on a broken save file till the end by just passing by the crash trigger.