The percentage is based on the voltage of the battery (the closer it gets to fully charged, the higher the percentage of charge). But, in order to fully charge it, the charger has to supply higher voltage that the fully charged battery will have. (That's just how electricity - it's like water only runs downhill - current only flows to a lower voltage.) When you charge it and it says 100%, that's a combination of the battery and the charger. So let it charge for another 30 minutes. Then it'll really be fully charged.
(If you leave it turned off for a week, then turn it on, it still won't be at 100% - for 2 reasons. First, almost all rechargeable batteries self-discharge. Not much, but after a week, you'll notice 1 or 2% less charge. Second, the phone, even when it's off, draws a little current. That's why it's able to turn on when you press the power button. It's not like a light switch that disconnects the phone from the battery, it's a circuit in the phone that monitors the switch and, when you press it for a few seconds, turns the phone on. PCs work the same way - they draw power when they're turned off.)
So fully charge it (30 minutes after it first says 100%), then don't worry about it.