I have an approximately 4 ft tall baby nectarine tree. Some, but not all, of the fruits, have large areas of missing skin, and deeply damaged dark interior sections.
I live in zone 9b in Northern California.
What could be the problem?
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Coryneum blight is also called shot hole disease - This is a fungus issue - Spray with a2-5% Chitosan solution as a tree drench - remove fruit that have dropped or developing fungus.
This is a guess until we have more information, ID of the thrip for example? Do you have any blooms left? This article tells you how to find the insects (they are tiny). A little specimen microscope and or a camera with micro capabilities.