technically there is no such thing as 100% charged, its just a value the phone company decides charge should stop, lets just talk about battery, a rechargeable battery that label 1.2v, you can overcharge it to 1.3-1.4v, when you stopped charging, charges will slowly go away, but if you overcharge it alot, you will lose those extra charge very fast, it will comes to stable at 1.2v and almost stopped discharging.

And for a battery, you will have no idea how many % its charged, you only know its voltage by measuring it, the voltage will slowly go down when its running low, so using previous example, a 1.2v rechargeable battery can be 0.1v to 1.4v, but if a device that label can use 1v, it wont function well if you just pass it 0.5v, so the usable voltage range for the device will be 0.5-1.4, if the device got an indicator, it will try to measure the current voltage and display it as %, it wont tell you the battery still have 0.6v(still got half), it will tell you 10% left, cause anything below 0.5v is not usable to the device.

For phone, they have some kind of battery protection, to avoid overcharging, basically to improve battery life, so the design will be, if the voltage of battery is ... lesser than 5v, charge it, and if more than 6v then stop charging. So your battery was at 6v, your charger stops, but your phone still drag power, it will slowly pull your battery down to 4.9v, your charger will turn on again. And if you ask why not lesser than 5v charge, and more than 5v stop, basically that will kill the battery or charger, as it will on and off very frequently.

So after long grandma story, the answer is your batter was just right below 5v when u turn it on. and if you still dont understand, sorry, i can no longer explain =P

btw the example 5v and 6v is assumption, the 1.2v rechargeable battery is true.