After fabrication but before installation at the factory, normally the ring and pinion gears are run in to achieve perfect (or near perfect) meshing of the front side of the teeth. Because of that, they are considered a matched set. On decelleration, the backsides of the teeth are loaded rather than the front side and because of that, whine if often the result. In addition, to make sure the tooth contact area is in the middle of the teeth, shimming of the pinion gear forwards or backwards is necessary. Shims for this are often .001" in thickness. If the assembly of the final drive wasn't done perfectly, tooth contact will be off and again, whining is possible. However, usually this is more pronounced under heavy load when accellerating.
Like several others said, drain the gear lube after riding. If it's possible, see if you can see any metal flakes in it. If you have a good magnet, swish it around in the lube to see if anything sticks to it. If there are shiny flakes, that's hard surfacing flaking off and that isn't good. If you suspect anything, take it to a dealer.