"Why didn't you ask?" dillema

D'you all know situations where people say: "You should have just asked about this."
But it's a situation you didn't even know there was knowledge you didn't have?

Example
We have files (on paper) about topic X. X is only relevant in folder A.
So, whenever I have a file about X I put it in folder A.

Sometimes there isn't much space left in the usual folder, so I put the files on top of the folder (people know where the folder is. And what's inside, etc, and it get emptied semi-regularly.
Today a colleague almost yelled at me for putting those those files on top of the folder, instead of requesting a new folder. And I was confused, because... what's the point? And he said, what if you're not here and someone confuses those papers with Y?
And I told him, because A is only ever relevant to X.

And then he said: But why didn't you ask me?
To which I answered what I described above. And only the did he tell me, that X can also be relevant in one other location I was never informed about. Which I told him then.

And then again he said: But why didn't you ask me?

Like... how?
How am I supposed to know I even have to ask a question?

This happens so often in my life. Is there some unspoken rule about this? Am I missing something? How do I know when to ask a question, when I don't have a question? And then what do I ask if 8 don't know if I should have a question and what it would even be about?