You need to use the following syntax
yes? fill 't'[k=1,l=1]
This is because ferret treats t variable name as time and to distinguish your variable name (if it is the same in the file), you have to provide it in double quotes.
TL;DR: It is not a problem, it is a feature.
As it was pointed in the comments, 1000 hPa over land (and sometimes over ocean) is below the surface. MERRA is just fair enough not to put any values where they do not exist. Other reanalyses use some procedure to fill the gaps and make fields without holes. The procedure is reanalysis specific, and, can ususlly ...