Not only will it not hurt the battery, it will actually help it last longer.
Li batteries do not like being fully discharged (or even close to it), or charged to 100% capacity, on a frequent basis.
Electric cars, like the Volt and the Leaf, keep the battery between about 25% and 75% charge under most operating conditions to prolong battery lifespan for just this reason.
The stock charging circuit in our phones prevents overcharging, unless you do the "bump charging" thing, which really is bad for your battery. Charging it multiple times during the day, to less than 100%, prevents the heavily discharged problem.