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There is a small problem with profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2 :
It isn't incomplete. So if one uses it to test the ability to detect and remove observation rows that have just missing values, there are no such rows to be discovered.

trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.nc
file from your collection of sample files.

For alt, the metadata has missing_value = -999.0f .
But the alt data has values of -999.9f.

lat,lon,alt,time,temperature,salinity,trajectory
39.491425,-35.10078,0.0,0,37.631386,52.763836,0
39.491425,-35.10078,1.0,0,20.998404,34.70631,0
39.491425,-35.10078,2.0,0,15.13594,25.764328,0
39.491425,-35.10078,3.0,0,31.464115,43.157772,0
39.491425,-35.10078,4.0,0,20.991987,62.27547,0
39.491425,-35.10078,-999.9,0,-999.9,-999.9,0
39.491425,-35.10078,-999.9,0,-999.9,-999.9,0
39.491425,-35.10078,-999.9,0,-999.9,-999.9,0

trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.nc
in your collection of sample .nc CF files:
For alt, the metadata has missing_value = -999.0f .
But the alt data has values of -999.9f.

row,lat,lon,trajectory,alt,time,temperature,salinity
0,5.875832,-19.151413,0,0.0,0,22.367708,4.9304028
1,5.875832,-19.151413,0,1.0,0,32.348286,27.114841
2,5.875832,-19.151413,0,2.0,0,13.822979,1.9672961
3,5.875832,-19.151413,0,-999.9,0,-999.9,-999.9
4,5.875832,-19.151413,0,-999.9,0,-999.9,-999.9

trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.nc
in your collection of .nc CF DSG sample files:

The rowSize variable has
rowSize =
{24, 24, 24, 24, 35, 35, 35, 35, 30, 30, 30, 30, 45, 45, 45, 45, 14, 14, 14, 14} which I sum up to be 592 rows.

But the obs dimension's current size is 641 and the z, temperature, and humidity variables which use it seem to have 641 valid values.
So there are 641 rows of data, but identifying information for only the first 592 rows.

I note that all 4 sample trajectory files have
trajectory_info=-2147483647
for all trajectories, and yet that value is not identified as a missing_value or _FillValue. So this isn't wrong, but maybe it isn't what you intended or very useful as a test that trajectory_info is properly assigned to the correct trajectory.

No examples for single stations

the variable with attribute cf_role = "profile_id"

profile-Indexed-Ragged-MultipleProfiles-H.3.5.nc

The index values in parentIndex range from 1 through 6, clearly intending to refer to the 6 profiles.

But the CF 1.6 standard
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp6503408
says "The index variable contains the zero-based index of the feature to which each element belongs" and the example's index values are 0 through 3.

So I think the parentIndex values in your sample file should range from
0 through 5.

No data variables are seen for H.2.1 by the tools-ui program.