That's possible, I suppose but more likely:
Overcharing lithium batteries is really bad. So bad that well designed devices turn off charging when the capacity is reached. At this point, I believe one of two things can happen. The device might be powered by the charger, however with the battery no longer receiving any charge, or (easier) the device can run on the battery after the charger has been disabled. The plug icon in the battery icon indicates charger not charging but connected. I think the iPhone is smart enough to run off the charger while not charging, however batteries can lose charge over time even when they are not being used.
The computer takes longer to charge the battery so it spends less time connected but not being charged than when you use the wall plug. I've seen this on a Palm PDA as well, although a little more dramatic. I believe the Palm was not smart enough to run off the charger and instead ran of the battery. Depending on when you disconnected, it could be truly fully charged or a few % low.