The support for NetCDF files in GeoClaw assumes something about the names of variables in the files to identify the correct variables to read. Right now this fails if those assumed are not found. One example of a file that currently does not work can be downloaded from
https://www.ngdc.noaa.gov/metaview/page?xml=NOAA/NESDIS/NGDC/MGG/DEM/iso/xml/5230.xml&view=getDataView&header=none