In the thought bubble, Kyouko actually says "youkai" in kanji, but says "person" in the furigana.
I never know which translation to go with when people do that. Does this mean she thinks "youkai" and the text is just clarifying that she's using it like "person"? Does it mean she thinks Kogasa is a human?
And even if I did know, I wouldn't know how to represent it... Haaah.

I'd go with translating the furigana, as that's what's assumed to be said aloud. Then either put the kanji translation in parens afterwards (in this case, "person (youkai)") or use a translation note if it requires a bit more explanation.

The furigana is definitely what's being said out loud. Presumably this is just the normal use of "hito" as "person" in casual speech. However, it'd be incorrect to use the kanji for "hito" because that literally means "human" which is being directly contrasted with youkai in the story.

Honestly I think you could just use the word "person" and leave it alone.