Spectral plot shows more notes than there really should be I was experimenting with sound analysis lately and from what I see when I plot spectral data of an audio file is that apart from notes that were actually picked there are some other notes with quite high local amplitude.
For example I have a sample where D major chord is played with some nasty distortion. After looking onto the spectral plot I can observe a note D, F# and A as expected. But as I go higher some other notes have higher amplitude than threshold, one of those is E.
Tried same algorithm for recorded guitar chord without distortion, but it sounds like there are some other effects like chorus or flanger and again additional note was found.
So, the question is: why I can see additional notes when analysing spectrum even though they were not picked during recording ?     

Note: The note E has some harmonics further in spectrum, so it cannot be treated like noise.
Since the notes from a guitar are no pure sinusoids, you should expect to see some harmonics, even when analyzing the dry signal without effects. E.g., the note E is the perfect fifth of the note A, i.e., it is the second harmonic.

If you use distortion or modulation effects (chorus, flanger, and phaser) you get even more additional frequencies due to the non-linearity (distortion) or due to time-varying filtering (modulation effects).

So in sum there are three sources of additional frequency components different from the fundamental pitches:


harmonics (due to non-sinusoidal signal)
non-linearities (e.g., overdrive/distortion)
time-varying filtering (e.g., modulation effects)


And in your example you get all three of them.