Some sand beds can develop a black spot that is up against the glass within the sand bed itself.  This is typically just cyanobacteria that is growing there as light is reflected down onto the sand surface through the glass.  It is not anything to worry about, cyanobacteria plays an important part in a marine aquarium (it is just when it reaches bloom proportions that it can be a problem, as with any organism).

If the spot is not black, but more grey in colour and diffused through the sand bed, then this is something different.  This grey/black colouring is the signature of that region of the sand bed going anaerobic.  That in itself isn't as big of an issue as it might sound, a sand bed going anaerobic is not a cause of concern.  It is only of concern when that area is exposed to the systems water, if it stays unexposed, within the sand bed, then it will not cause any problems. 

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