The reason for this screw up was guessed by a Twitter user, and his theory was confirmed by Josh from Let's Encrypt [1].
The whole mess was caused by the Python `email` package, and specifically the behavior of the `MIMEMultipart` object [2]. When you reuse the same `MIMEMultipart` object for multiple emails, each destination address is appended. The same problem takes place when you use Python 3 [3].
[1]: https://twitter.com/0xjosh/status/741487697059946497
[2]: https://docs.python.org/3/library/email.mime.html#email.mime...