Yep, it was my fault in the first place with the autosave option off :\
Similar thing happened to me except I was lucky and never had any glitch. I turned off all autosaving and my game loads so much faster it's ridiculous. Anyway I had forgotten to save after doing all this work and I thought I'd muck around and kill some guards. Usually I save before going on a killing spree but I just completely forgot. I still left autosave off for now but now I save more often. I don't know if the auto-save actually saves time but to me it does.