People catch on to thing at different rates, some cant comprehend thing that you find simple. That's just people being people everyone is different which can be troublesome. Such as the amount of people who have got stuck on Bensons route, which is a majestic amount, despite every character in the bad end saying the word multiple time one after another and people still not noticing.
Sometimes sacrifices have to be made regarding writing simply to be as inclusive as possible. I don't mean that in the 'dark souls: oh its just too hard for you just say away' elitist nahhaha, way. But trying to make something that everyone interested in it can enjoy means setting the bar to the most common point. (god reading all this back makes me sound so snarky and condescending its shameful that I cant think of another way to reword this)
If the majority cant overcome a certain point in the story, the story needs to be adjusted in some way usually by making sacrifices. Of course the story should only be sacrificed to a point, such as in the Benson bad end, the answer is given is such a way it could be put on a neon billboard, there isn't much more that could be done to make it more clear without just straight up saying it.
These things happen and need to be accounted for but its up to you how far you want to bend over backwards for. No matter the choice when everything is finished up or more complete I have no doubt someone will make a full walkthrough for those who don't mind spoilers so I wouldn't worry too much about it in the long term, as disheartening at it may be in the short term.