After completing the upent quest where I have to set a bomb on 4 upents, the quest claimed to have rewarded me with Torn Diary Part 3 and Part 4, but in my inventory I have two Part 4’s. How am I supposed to follow the story if you don’t give me Part 3???
you don’t get part 3 from that quest, you get it from the well quest if I remember correctly …
Oh um… How did I get part 4 without getting part 3 first then?
because you didn’t completed the well quest before doing the upent one :\
got it now?_?
EDIT: the game is less linear than everyone brains make it…
Why do you expect to receive the parts in linear order? In some games you get notes like that only describing a middle part wich you dont understand what is going on right. So you try to look for the other parts 
And then there is an area which has not a single NPC on it which gives you quests. Instead there is diaries books and notes all over the playes and to unravel what happened there you need to look around and actually find them. If youre interested that is.
And the well is more of a secret too. If you dont find it well, you miss out. Youre supposed to keep your eyes open, there is riddles secrets, chests that are visually obstructed and you only find them if you actively search areas where you wouldnt normally go.
But I guess the tunnelvision in beta is normal you want to progress as fast as you can don’t blame yourself for rushing.
Keep a few secrets that makes the game more enjoyable at OBT/release.