Yet you've used somebody's words to describe the problem.
In fact, it almost seems like there is no other way to describe such problems. They are conceptual, ephemeral, not wholly in the realm of things you can see or witness, but only really describe.
I'm not aware of anyone since Charles Sanders Peirce actually making a serious scientific effort to investigate this problem. His work is well worth the read for anyone who wants to see what semiotic looks like when one of the greatest logicians (I'm talking Frege tier) to live turned his mind to it.
On a New List of Categories[1] is a good entry point. I like How to Make Our Ideas Clear[2] as well, and it may be more germane to this topic. He was a prolific writer, and I've found everything of his I've read thought provoking.
Edit: Some Consequences of Four Incapacities[3] is another that deals with how we understand things.
In fact, it almost seems like there is no other way to describe such problems. They are conceptual, ephemeral, not wholly in the realm of things you can see or witness, but only really describe.