ERA5 reanalysis data on pressure levels at lower levels, eg at 1000 or 850 hPa, can show atmospheric variables that are below the model terrain. This happens in regions such as the Himalayas or Andes and is due to the interpolation of data from model to pressure levels  (the interpolation documentations is at http://www.umr-cnrm.fr/gmapdoc/spip.php?article157).
The data which is below the surface can be masked out using the surface pressure or the surface geopotential.
For more information about ERA5 levels see the ERA5 documentation.