Translation:I have only read one of those thirteen books.
I am likewise an English native (AmE), and I'd probably default to "I have only read one...," though if I were feeling particularly "grammatical" I'd switch to "I have read only one..." To my ear, they are equally natural. Are you, by any chance, native BrE? Sometimes we run across unexpected usage differences between the two.
I am BrE bit lived away for over 35 years,, so my English is now pidgeon English, but really in this instance they are identical and i shouldnt have been marked wrong. Unless it is a specific Czech language thing whereby that should be explained and given correct just like the spelling mistakes are :)
This may sound weird, but it occurs to me, on re-reading your earlier comment, that your answer may have been rejected because of the "13" in it. If I recall correctly, numerals may have to be added manually. And when there are sentences with hundreds -- even thousands -- of possible translations, it's easy to miss something.
PS for others learners:
The Report button is your friend. It sends answers directly into the system, so the course team can see exactly what you wrote and can then (usually) tell you exactly why what you wrote was not accepted.