His one Sharingan was surgically implanted sometime in the past. Yes, this must mean someone gored out one of the dead Uchiha's eyes and decided to experiment on Kakashi with the idea, but who knows.

Or the scar over his eye could be from someone trying to cut his eye out (like Zabuza wanted to do) and had failed, and he's really some kind of half-breed between an Uchiha and someone else, which is why he has an imperfect version (and only one).

And no, I don't read the manga so that whole thing is one big speculation on my part.