As a nice guy who’s managed to be married for more than 30 years now, I can decode this for you.
“There’s nothing actually wrong with you, but I have zero attraction toward you.”
Of course, this is completely shattering to a teenager (boy or girl) but on the bright side, it’s also nothing personal.
The only way I can describe it is by metaphor.
Sometimes you studied hard but the test asked different questions.
Sometimes you’re set for a fastball but the pitcher throws a curve.
Assuming they’re actually nice and not “Nice Guys” things will click for them eventually.