You just reminded me that you can miss a complete optional yet lenghty and rewarding dungeon area which has also ties to the main story (and some funny easter eggs altogether) in Tales of Vesperia if you don't happen to travel all the way to a certain part you've already visited in the world, in a crucial plot story moment, despite what common sense might tell you. It's baffling, and there's no second chances; proceeding forward the story and coming back won't trigger it. So I can say I totally relate to that one.
I'd say people with Plot Armor in these "your choices will affect the outcome of the story" kind of games is what I find most conflicting. I know there's got to be some kind of anchor so that the story doesn't get extremely weird because the plot character isn't where he or she should be, but sometimes it just don't make sense, and I don't understand why the devs didn't think of a workaround of it. The most notable examples? Ethan Mars and Scott Shelby in Heavy Rain or Mike in Until Dawn. There's entire subtplots that rely on the character being alive, and the game will do whatever it can to achieve that, thus giving the player the biggest illusion of choice they can. As a result, there are scenes that lack any kind of proper resolve or logic. Try getting Ethan killed during the Butterfly trial, for example (Heavy Rain spoiler), or expose Mike to any danger you can prior to the final cabin sequence (Until Dawn spoiler). They're simply unkillable, and the game will conveniently skip the chapter altogether and just give a bullshit excuse (or just don't explain anything at all) and the game carries on like normal.
