This game has its fixed path to complete the story, its not like open world rpg even though it looks like open world... when u do something different tasks like eating when not necessary or sleeping unnecessarily or skipping any task, those bugs will appear... u can obseve that like, eg. clipping two scenes on each other, missing quest elements in inventory, etc
I would recommend follow the walkthrough pdf as it is... load nearest point from default saves and start as it is shown in pdf, and to be honest i hv completed android version according to walkthrough pdf without any issues. Good luck!!