Is this game annoying on purpose? or just bad game design?

I fell into the whole that I've seen others all into of not reading the newspaper near the start of chapter 1, so I can't complete it without starting over.

Is this a common theme in the game?

I'm not too thrilled about having to replay the entire chapter to fix a problem that I had early on, that I didn't know I had until I've played the game for almost an hour and a half.

If I had found out about this at the 20 min mark, maybe. But already 90 min, which people are saying is maybe 10% of the game? That is a lot of replaying the same garbage without skipping cut scenes.

It's not bad game design at all. There are multiple endings, and the game has multiple save slots for each chapter. Except for Chapter 5, I can't imagine why you would ever need to restart from the beginning if you aren't erasing all of your old saves.

Moreover, it's really not a hard wrong ending to avoid. You get a mysterious key, and by that point in the game there just aren't that many mysterious doors to unlock.

The only "bad game design" is the design to not include a fast-forward feature for dialogue you've already read, which is admittedly kind of annoying. Thankfully, most of the chapters are fairly short, so that mitigates some of the inconvenience involved.

If it makes you feel any better, though, most of the chapters will warn you in some way before you do something that gives you a wrong ending. Read everything, including all of the signs on the walls, unless the game tells you otherwise.

I don't even recall seeing a mysterious door to work with that key.

Most games gives you multiple slots, usually it's pointless to do so unless there is a specific point in the game you want to replay over and over again (opera house sequence in FFVI, for example).

So I'm used to just resaving games on top of my prior saves.

Maybe it's just this story-native format of game I'm not used to.

I'll probably try it again and take note of everything I may have missed, but since I have to sit through about 40 min of dialog that I've already read, I can see my self dozing off in the process and causing me to miss the exact thing that was missed the first time.

You do know that, you can just walk over and pick up the key and then go read the newspaper, at any point in the chapter, you don't have to start over. Unless you saved yourself into a corner, but I don't remember if that was possible.

Does that mean you got the ending where
Naomi get's her tongue cut out?
If so I would consider you lucky.

But yes, the game will try to do this to you on purpose,
you will have to be aware of it. Multiple save slots are encouraged.