Mine did the same about 3 times over the first 8 or so months I had it, with the battery completely discharging when left for more than a few hours in "sleep" mode. I don't use the WiFi on the reader, and that is always switched off, nor do I use the audio - the only functions ever used are just reading ones, mostly epubs.
If I am not going to next use the reader within an hour or so, I now always turn it completely off - by doing so I have not had the problem repeat itself (so far anyway
So seems to be some software matter either in the firmware or initiated in some way (I could not guess what way) by the book that was open when the reader was switched to "sleep" mode. It didn't happen enough times for me to draw any conclusions, but if the latter was the case then I wouldn't be surprised if it had been more frequent with pdfs.
In any event, it is something to be avoided as deep discharges shorten the life of most batteries, including Li-ion/polymer ones.