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The holes are places where the data was 0,0,0 RGB and then gets mapped to transparent/NODATA. You can define an area in ArcMap and replace all NoData values with 0,0,1 or something like that to fill the areas in if thee pixels are a problem.
This usually only happens when there are super hard shadows. True black 0,0,0 doesn't happen very frequently in camera sourced imagery which is why it is used. That, and the surrounding areas are black in our GeoTiffs before we remap it.