So I just heard Neon by John Mayer and decided to learn the main riff, but it seems that for a certain part, it has two guitars in it.

0:37-0:46 in this

That sound's not anywhere else in the song, and it does sound like there's a second guitar, but I've heard that one reason Neon's so impressive is because it sounds like there's two guitars when it's only John playing.

The noise sounds like a second guitar repeating everything the first plays after a very short delay, but the notes are more percussive and have less tone.