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Strange tone

So I'm playing through a bass riff I made, and I just noticed something strange. I'm playing unplugged, which I dont do often so I'm not sure how long this problem has been here, but when I hammer on the 12th fret of the A string, it produces the A note but then an A# note rings out beneath it. If I hold it down then pluck it, it sounds fine, but only if i hammer on does it make the strange noise. Does anyone know what this could be? I'd be embarassed if it's a tuning issue, but I want to make sure it isn't something major wrong with the fretboard or something.
 
It's the string vibrating behind where you're fretting - i.e. the section of the string between the nut and the fretted position. The note produced there is A#. Just damp it.
 
You're only hearing it on a unplugged because both sounds are the same volume. On an acoustic instrument or a plugged in electric, the A would be amplified, and far, far, far louder than the A#.

The way to "fix" it is to play plugged in. Do you play unplugged at rehearsal or at a gig?