Did they play when you tested on your device prior to release in the iBook store? I have heard reports that MP3s do not work, but I was unable to reproduce the problem. (I also have never published in the iBooks store).
In Apple's official support they now appear to be advising that people use the m4a file extension and to encode in AAC:
For audio, use AAC (8 to 320 Kbps, 48 kHz stereo) with an .m4a file extension.
via this support page
They also advise:
If a movie or audio file doesn't play in your widget in iBooks Author, preview it on your iPhone, iPad or Mac. This shows how the file will play in your completed book.
So if during testing it plays but not when loaded in the iBooks store then there's a weird bug going on in the publishing process.
The HTML widget object in iBooks Author is a wrapper for Mobile Safari so you should see the same behavior between Mobile Safari and HTML widgets except for specific pinch gestures which the HTML widget overrides.