Most of those aren't bugs - they were elements that were intentionally added (fake talking tree branch) or that make logical sense (if you kill someone, you can't get item x from them or complete a quest they are involved in). There are a few real bugs, though most were fixed in the patches.
I guess you could argue that Larian should have just made it so you couldn't sell/lose quest items, or that you couldn't kill/anger NPC's.
Luckily we have forum members who are willing to offer fixes for almost every one of the issues.
