GDAL has some limitation concerning the reading of netCDF4 files.
Most of the tests were done on a personal computer using QGIS 2.12.1 and GDAL 1.11.3.
- Gdal can't read correctly netCDF lat/long values if there is not an exact spacing between points (pixel). For example: use a exact spacing of 0.2 degrees.
- Gdal reads misplaced lat/long grid in netCDF4 files. It reads 0 to 360 degrees instead of -180 to 180 degrees. But I think that this can be solved setting a parameter (pm=-180 or pm=180) in projection definition in QGIS or MapServer.
- Gdal displays netCDF files upside down: http://lagerratrobe.blogspot.ca/2009/02/upside-down-netcdf-created-with-gdal.html
- Gdal can't detect if data are wrtitten bottom up or bottom down, so when reading netCDF files, to get statistics and pixel values we must change a configuration of Gdal.
- GDAL_NETCDF_BOTTOMUP=NO, See https://trac.osgeo.org/gdal/ticket/5291, https://trac.osgeo.org/gdal/ticket/5082 and http://osgeo-org.1560.x6.nabble.com/Problems-with-GDAL-1-10-1-converting-from-NetCDF-to-Geotiff-td5180197.html