Hi Cian,
no major reason; or rather, a ton of small issues could have caused this:
- connexion error while downloading
- bug or crash during a "dataset building script" (there was a lot of moving data around in the beginning)
- the song didn't have EchoNest beat because they could not be computed
- the song didn't have EchoNest beat because of a bug / issue
- … and I'm probably forgetting some
The MSD is real data, and real data is messy. I wouldn't read too much into it, unless you find a correlation with other features (e.g. small duration, a specific genre, …)
Cheers!
Thierry