Using the NetCDF raster layer as input to the raster clip geoprocessing tool gives incorrect pixel values for the clipped output.
This is a known issue.
There are two workarounds to this issue:
- Use the Extract by Rectangle tool (Spatial Analyst Tools > Extraction) on the NetCDF raster layer. This works fine and gives the correct pixel values for the clipped output.
- Export the NetCDF raster layer into a permanent raster and use the Clip tool. This gives the correct pixel values for the output.