An investigator in Japan, where a 787 made an emergency landing earlier this week, said the charred insides of the plane’s lithium ion battery show the battery received voltage in excess of its design limits
This investigator may have inside information but I very much doubt anyone can tell the cause from just looking at photos of the burnt remains!
Overdischarge can also cause problems for some Li cells when it's next charged. This is just one of the things that the charging circuit will check (eg that it's not too empty to be charged safely).
NPO19897 :: NASA Tech Briefs
"..overdischarge can result in dissolution of a metal current collector in the anode of a cell, with consequent internal short-circuiting of the cell..."