Was this work done on data stored in lossy formats? The appendix with the talk about format conversion makes it sound like it. Should this not have been the first thing to be avoided („garbage in, …“)?
You're right to mention this. Lossless audio is preferred for analyst software. Even good MP3s tend to top out around 16kHz.
The quality of the recording will also be dependent on the microphones used and their frequency range.
When we have analysed animal sounds it's useful to play the sample slower, pitched down. Having those higher frequencies recorded well, above 16kHz, make a huge difference to the signals information.
A more meaningful criticism would be the use of the wigner transform itself, which seems to produce ringing artifacts in the visualization, not seen on the more common windowed fft.
(Filter by WAV, FLAC, or AIFF.)
https://freesound.org/search/?q=Eastern+Wood+Pewee
1 result
https://www.xeno-canto.org/explore?query=Eastern%20Wood%20Pe...
228 results
Furthermore, your search for blackbird on Freesound gives 639 results based on a text match, while xeno-canto gives 7449 results from 32 species, with metadata tagging it by species, location, date, time of day.