I just finished killing Tchort on my first playthrough, and when I returned to SGS to check on things I noticed that the transition to Level 4 (and only that level) is bugged, and fails (I went there to talk to Vera about Lora about what happened in DC). A couple of other strange things happened earlier too, which makes me think there's maybe something wrong with my save file, as Steam validation checks turned out normal. There were no other crashes or similar errors in over 110 hours.
The first strange thing is the one I don't have a screenshot for, but I looted a component relatively early in the game (during the Hijacked Train thing, IIRC) that was simply a square yellow box with a ? inside it. I have it stashed somewhere, but I can't remember where. The second one is the Mutagen puzzle below, which seems broken to me (and to the solver tool), but I concede there's a possibility it's solvable and I just can't see it. Almost went crazy over that one.
Then, finally, the transition error mentioned above, for which I provided the latest log (there are other logs, but they seem identical to me), and the screenshots of both the fail screen itself, and the error that happens if I try to load the autosave it generates. The .zip with the save file folder was too large to attach, but I uploaded it via the link below.
www sendspace com /file/3lew2i