I think the real problem lies in the doubling of that vocal. The pitch discrepancy between the two takes of him singing that note is too great, and it really calls your attention to the flatness of one of the takes (think Anthony Kiedis).
At the end of the song, he sings a higher note, and it's not doubled. It's not perfectly in tune either, but because it's by itself, it sounds just fine.
Also, after 20+ years of auto-tune, our ears are more persnickety about pitch than they used to be.