Boot into recovery, perform an FDR. This has always fixed this issue for me on my N4 and N5.
I've just made an FDR my final step after I flash a factory image...helps avoid this problem all together.
What you are hearing (to some degree) is completely normal. You are hearing the audio chip powering down after a sound has played. This is to conserve battery life. Almost all mobile phones employ a similar technique.
Just discovered that my prime is almost an index finger off in accuracy around the inner 1" edge of the screen. Causes me to keep missing the search button in the browser, it registers me clicking the bookmark button instead.