pippiLs, I think you are expecting too much, and worrying too much! But I've been there so I understand.
A brief history of time, and similar, such as the current books on Einstein's work, is aimed at a low reading age, for a very good reason,
It is excellent that you are reading together, that is important, and breif history of time gives you plenty to discuss, which is actually more important to his development than reading!
I didn't bother with the reading logs at primary school just partially filled them in to keep the teacher quiet, but made no attempt to write down everything.
These levels are inaccurate, and meaningless. I once turned over the list a previous teacher had given me, so matching the top name of the register to the bottom score on the list, etc. it fitted better that way round , so I chose to decide that was the way round it was meant to be.
My son was an advanced reader, gifted in music with amazing scientific understanding at 7. Now 14 he is in a grammar school winging and complaining this morning that his sousaphone lesson is going to overlap with the lunchtime flirt by 5 minutes.
He benefited from me reading with him and discussing things with him, and taking a close interest in his schooling. Actually I still do, although he appreciates it less these days!
He also frequently messes up, avoids work, strops, forgets hw, fails to show his potential in exams, makes the most stupid mistakes, gets told off for chat, or answering back ....... Sometimes!
He also sometimes works hard, does well, and makes me proud.
In other words, yes he is clever, basically hard working , with potential and aspirations.
he is also a human teenage boy!
When the time comes, work with your son on 11+ papers. If he is clever, and practices, and has your support, he is going to be fine. Don't let this one tiny little incident make you despair, because, I promise you, there will be many.