This is quite common and not really a problem, I know what you are talking about I've had this sort of thing myself. what it actually is, is that when you play that note a sympathetic vibration is being generated from it, I know it sounds weird but it works like this, say you play a note on the high e string at the 12th fret, when it rings there is a sympathetic vibration coming from another part of the guitar, it could be a loose fret a spring, screw, or saddle component or a part of the fretboard etc. this can affect notes in different ways, sometimes it can cancel out the note altogether, a strange phenomenon admitted, a guitar tech could solve it for you or you could solve it yourself, sometimes its impossible to solve and you have to live with it. its more common with bolt-ons rather than guitars with fitted necks.