Due to how battery designed. A actually fully discharged battery can't be charged normally.(the power control chip on the battery need a bit power to function normally) Typically this can't happen because your phone will shutdown before that.
But if you used up the battery and not charge for a long time (1 months or so). This can happen because batteries discharge themselves slightly even not being used.
Why can't the power control chip also get power from the charging power? That wouldn't be particularly hard to do.
It turns out my memory is incorrect. The lithium-ion batteries damage itself when the under certain voltage due to how it works. The control chip is there to stop the battery from having too low voltage. However they can't help with self discharging caused low voltage.
Battery chemistry often relies on there being ~some charge. Completely dead battery would be, as the name implies; dead