The GEOS data assimilation system that is used to produce MERRA-2 does not extrapolate data pressure levels that are greater than the surface pressure. These grid points are assigned undefined, or missing, values.
If you are interested in data at the surface layer, you may want to look at the data with the model layers (lev=72) instead of pressure levels.
The figures are an example of temperature over 1000hPa and the surface pressure for Jan 2020 from M2IMNPASM_5.12.4. The surface pressure over most land regions is less than 1000hPa, thus the air temperature was assigned missing values.
https://giovanni.gsfc.nasa.gov/giovanni/#service=TmAvMp&starttime=2020-01-01T00:00:00Z&endtime=2020-01-31T23:59:59Z&data=M2IMNPASM_5_12_4_T(z%3D1000)%2CM2IMNPASM_5_12_4_PS&dataKeyword=M2IMNPASM
Related topics: Why are there such large discrepancies at 1000mb and 850mb between MERRA and other reanalyses?