If the file has several variables and some of them have different information, it could bother the CDO calculation.
So, it will be better to do it with the file with the single variable, or variables which have the same attribution, exactly.
cdo select,name=var1,var2, … ,varN input output
So, if you want to extract sea surface temperature (variable name: sst) only from my_data.nc then,
cdo select,name=sst my_data.nc new_data.nc
So, Simeple 🙂