Dear Client,

I am wondering if you had any hail over the past few weeks. If the damage is widespread on fruit closest to the perimeter of  tree and get less noticeable on the fruit on the inside of the tree, this would be another clue suggesting hail damage.

If you can rule out hail, the next source of the damage to consider is general insect damage that is caused by a larger insect with chewing mouthparts.  If the damage is concentrated on the lowermost fruit, moth larvae or caterpillars are an possibility.  Cutworms, armyworms tend to overwinter as near mature caterpillars that emerge early in the season and eat anything green- leaf buds, flowers, fruitlets.  Most other common pests of nectarine are not big enough to bite and surface bore into the tough little fruitlets. 

So these are two of the leading possibilities.  More investigation is necessary, but only if you are observing fresh new damage to the nectarines.  Then you might consider shaking the branches over a white net on the ground and seeing what large insect drops out of the tree.  Cutworms, armyworms would be most active at night and early in the dawn.  Until we figure out what is causing the damage, we can't prevent this damage. 

Hope this helps, sorry if it doesn't!