Hi,
I have exactly the same issue with a Macbook Pro Retina 13'' (mid-2014). It had Mavericks installed and upgraded to Yosemite just after purchase.
The system's battery % indicator is consistently about 3-5% higher that the "real" percentage. Understanding by real percentage the division between current charge in mAh and maximum charge in mAh, that is what apps like Coconut battery show.
Right now system shows 96% while cononut shows 91%.
I have tried calibration, SMC reset, NVRAM reset, as explained above. Nothing helped.
I have no idea what is happening but it seems clear that the system percentage is not the result of dividing current and max charge capacity. Maybe MacOSx applies some correction? (no linear division), but then, why only few users see this problem?
Another 'issue' that I am not sure if it is related or not: in my macbook is almost brand new, the maximum charge is deteriorating faster than normal, I think. When I bought it, battery was 3 month old from factory. Max capacity was 6350 mAh (100% of designed 6330mAh), but normally when brand new batteries have capacity higher than 6400.
After only 3 cycles capacity has dropped to 6200 mAh (98%).
Daniel